From 0e59906436651a95857b3aae8e6bf0cf79dbae54 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Dec 2025 17:26:44 +0000 Subject: [PATCH 01/11] feat: Add riboWaltz MultiQC custom content integration MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Add ribowaltz_to_mqc.py script to transform riboWaltz TSV outputs to MultiQC custom content format (psite regions, frames, metaprofiles) - Create local RIBOWALTZ_MQC module to run the transform script - Create RIBOWALTZ_QC local subworkflow to encapsulate riboWaltz logic - Update riboWaltz module to export underlying data as TSV for all QC plots - Add riboWaltz to MultiQC top_modules for proper section ordering - Configure publishDir for riboWaltz outputs (QC to riboseq_qc/, coverage to other/) The MultiQC integration includes: - P-site region distribution bar chart with RNA-seq reference - Reading frame distribution grouped by transcript region - Metaprofile line graphs for start and stop codons 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 --- assets/multiqc_config.yml | 1 + bin/ribowaltz_to_mqc.py | 227 ++++++++++++++++++ conf/modules.config | 20 ++ modules.json | 2 +- modules/local/ribowaltz_mqc/main.nf | 31 +++ modules/nf-core/ribowaltz/main.nf | 4 + modules/nf-core/ribowaltz/meta.yml | 15 ++ .../nf-core/ribowaltz/templates/ribowaltz.r | 42 ++++ modules/nf-core/ribowaltz/tests/main.nf.test | 2 + subworkflows/local/ribowaltz_qc/main.nf | 72 ++++++ workflows/riboseq/main.nf | 14 +- 11 files changed, 424 insertions(+), 6 deletions(-) create mode 100755 bin/ribowaltz_to_mqc.py create mode 100644 modules/local/ribowaltz_mqc/main.nf create mode 100644 subworkflows/local/ribowaltz_qc/main.nf diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 9c2737bb..594c349a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -48,6 +48,7 @@ top_modules: - "fail_trimmed_samples" - "fail_mapped_samples" - "fail_strand_check" + - "ribowaltz" - "star_rsem_deseq2_pca" - "star_rsem_deseq2_clustering" - "star_salmon_deseq2_pca" diff --git a/bin/ribowaltz_to_mqc.py b/bin/ribowaltz_to_mqc.py new file mode 100755 index 00000000..bbd2284d --- /dev/null +++ b/bin/ribowaltz_to_mqc.py @@ -0,0 +1,227 @@ +#!/usr/bin/env python3 +""" +Transform ribowaltz TSV output to MultiQC-compatible format. + +Usage: + ribowaltz_to_mqc.py psite_region > output.tsv + ribowaltz_to_mqc.py frames > output.tsv + ribowaltz_to_mqc.py metaprofile_start > output.json + ribowaltz_to_mqc.py metaprofile_stop > output.json +""" + +import sys +import csv +import json +from collections import defaultdict + + +def transform_psite_region(files): + """Transform psite_region.tsv files to wide format for MultiQC bargraph.""" + data = defaultdict(dict) + rna_ref = {} # Global RNA-seq reference from annotation + regions = ["5' UTR", "CDS", "3' UTR"] + + region_map = {"5' UTR": "5' UTR", "5utr": "5' UTR", + "CDS": "CDS", "cds": "CDS", + "3' UTR": "3' UTR", "3utr": "3' UTR"} + + for filepath in files: + with open(filepath, 'r') as f: + reader = csv.DictReader(f, delimiter='\t') + for row in reader: + sample = row['sample'] + region = row['region'] + clean_region = region_map.get(region, region) + + # Capture the 'RNAs' reference (same for all samples using same annotation) + if sample == 'RNAs': + if clean_region in regions and clean_region not in rna_ref: + rna_ref[clean_region] = float(row['scaled_count']) + continue + + if clean_region in regions: + data[sample][clean_region] = float(row['scaled_count']) + + samples = sorted(data.keys()) + + # Output YAML header + print("# id: 'ribowaltz_1_psite_regions'") + print("# section_name: 'P-site Region Distribution'") + print("# description: 'Distribution of P-sites across transcript regions. Good Ribo-seq data shows strong CDS enrichment (>70%). The RNA-seq reference shows expected distribution from uniform transcript coverage.'") + print("# parent_id: 'ribowaltz'") + print("# parent_name: 'riboWaltz'") + print("# parent_description: 'Quality control metrics from riboWaltz for assessing Ribo-seq data quality.'") + print("# plot_type: 'bargraph'") + print("# pconfig:") + print("# id: 'ribowaltz_1_psite_regions_plot'") + print("# title: 'riboWaltz: P-site Region Distribution'") + print("# ylab: '% of P-sites'") + print("# cpswitch: false") + + # Output data + print("Sample\t" + "\t".join(regions)) + + # Output RNA-seq reference first if available + if rna_ref: + values = [str(round(rna_ref.get(r, 0), 1)) for r in regions] + print(f"RNA-seq reference\t" + "\t".join(values)) + + for sample in samples: + values = [str(round(data[sample].get(r, 0), 1)) for r in regions] + print(f"{sample}\t" + "\t".join(values)) + + +def transform_frames(files): + """Transform frames.tsv files to MultiQC custom content. + + Structure matches ribowaltz frames.pdf plot: + - Groups: regions (5' UTR, CDS, 3' UTR) - using sample_groups + - Within each group: one bar per sample + - Each bar stacked: Frame 0, Frame 1, Frame 2 segments + + Key QC insight: CDS should show Frame 0 enrichment, UTRs should not. + """ + data = defaultdict(lambda: defaultdict(dict)) + frames = ["Frame 0", "Frame 1", "Frame 2"] + regions = ["5utr", "cds", "3utr"] + region_labels = {"5utr": "5' UTR", "cds": "CDS", "3utr": "3' UTR"} + + region_map = { + "5' UTR": "5utr", "5utr": "5utr", + "CDS": "cds", "cds": "cds", + "3' UTR": "3utr", "3utr": "3utr" + } + + for filepath in files: + with open(filepath, 'r') as f: + reader = csv.DictReader(f, delimiter='\t') + for row in reader: + sample = row['sample'] + region = region_map.get(row['region'], row['region']) + frame = f"Frame {row['frame']}" + if region in regions and frame in frames: + data[sample][region][frame] = float(row['scaled_count']) + + samples = sorted(data.keys()) + + # Output YAML header + print("# id: 'ribowaltz_2_frames'") + print("# section_name: 'Reading Frame Distribution'") + print("# description: 'Distribution of P-sites across reading frames for each transcript region. Good Ribo-seq data shows Frame 0 enrichment (>50%) in the CDS but not in UTRs.'") + print("# parent_id: 'ribowaltz'") + print("# parent_name: 'riboWaltz'") + print("# parent_description: 'Quality control metrics from riboWaltz for assessing Ribo-seq data quality.'") + print("# plot_type: 'bargraph'") + print("# pconfig:") + print("# id: 'ribowaltz_2_frames_plot'") + print("# title: 'riboWaltz: Reading Frame Distribution'") + print("# ylab: '% of P-sites'") + print("# cpswitch: false") + + # Build sample_groups: group by region, with samples within each region group + # Structure: {"5' UTR": [["sample1_5' UTR", "sample1"], ...], "CDS": [...], ...} + if len(samples) > 0: + print("# sample_groups:") + for region in regions: + label = region_labels[region] + print(f'# "{label}":') + for sample in samples: + # [sample_key, display_label] - display_label is the sample name + print(f'# - ["{sample}_{label}", "{sample}"]') + + # Output data: each row is {sample}_{region} with frame values + print("Sample\t" + "\t".join(frames)) + for sample in samples: + for region in regions: + label = region_labels[region] + row_id = f"{sample}_{label}" + values = [str(round(data[sample][region].get(f, 0), 1)) for f in frames] + print(f"{row_id}\t" + "\t".join(values)) + + +def transform_metaprofile(files, region_filter): + """Transform metaprofile_psite.tsv files to MultiQC linegraph JSON format. + + Args: + files: List of metaprofile TSV files + region_filter: "start" or "stop" to filter by region type + + The input TSV has columns: sample, region, x, y + Region values are "Distance from start (nt)" or "Distance from stop (nt)" + """ + data = defaultdict(list) + + region_map = { + "start": "Distance from start (nt)", + "stop": "Distance from stop (nt)" + } + target_region = region_map[region_filter] + + for filepath in files: + with open(filepath, 'r') as f: + reader = csv.DictReader(f, delimiter='\t') + for row in reader: + sample = row['sample'] + region = row['region'] + if region == target_region: + x = int(float(row['x'])) + y = round(float(row['y']), 2) + data[sample].append([x, y]) + + # Sort each sample's data by x value + for sample in data: + data[sample].sort(key=lambda point: point[0]) + + # Build JSON output + if region_filter == "start": + section_name = "Metaprofile (Start Codon)" + description = "P-site frequency around the start codon. Good Ribo-seq data shows trinucleotide periodicity with peaks at frame 0 positions." + plot_id = "ribowaltz_3_metaprofile_start" + xlab = "Distance from start codon (nt)" + else: + section_name = "Metaprofile (Stop Codon)" + description = "P-site frequency around the stop codon. Good Ribo-seq data shows trinucleotide periodicity with peaks at frame 0 positions." + plot_id = "ribowaltz_4_metaprofile_stop" + xlab = "Distance from stop codon (nt)" + + output = { + "id": plot_id, + "section_name": section_name, + "description": description, + "parent_id": "ribowaltz", + "parent_name": "riboWaltz", + "parent_description": "Quality control metrics from riboWaltz for assessing Ribo-seq data quality.", + "plot_type": "linegraph", + "pconfig": { + "id": f"{plot_id}_plot", + "title": f"riboWaltz: {section_name}", + "xlab": xlab, + "ylab": "P-site frequency", + "x_decimals": False + }, + "data": dict(sorted(data.items())) + } + + print(json.dumps(output, indent=2)) + + +if __name__ == "__main__": + if len(sys.argv) < 3: + print(__doc__, file=sys.stderr) + sys.exit(1) + + mode = sys.argv[1] + files = sys.argv[2:] + + if mode == "psite_region": + transform_psite_region(files) + elif mode == "frames": + transform_frames(files) + elif mode == "metaprofile_start": + transform_metaprofile(files, "start") + elif mode == "metaprofile_stop": + transform_metaprofile(files, "stop") + else: + print(f"Unknown mode: {mode}", file=sys.stderr) + print(__doc__, file=sys.stderr) + sys.exit(1) diff --git a/conf/modules.config b/conf/modules.config index e426d60d..ee1054a8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -920,6 +920,26 @@ if (!params.skip_ribowaltz) { process { withName: 'RIBOWALTZ' { ext.args = { params.extra_ribowaltz_args ?: '' } + publishDir = [ + [ + path: { "${params.outdir}/riboseq_qc/ribowaltz" }, + mode: params.publish_dir_mode, + pattern: "{ribowaltz_qc,offset_plot}/*", + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ], + [ + path: { "${params.outdir}/riboseq_qc/ribowaltz" }, + mode: params.publish_dir_mode, + pattern: "*.{best_offset.txt,psite_offset.tsv,psite_offset.tsv.gz}", + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ], + [ + path: { "${params.outdir}/other/ribowaltz" }, + mode: params.publish_dir_mode, + pattern: "*.{psite,codon_coverage_rpf,codon_coverage_psite,cds_coverage_psite,nt_coverage_psite}.tsv{,.gz}", + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + ] } } } diff --git a/modules.json b/modules.json index 89ea4fd3..9f42ae93 100644 --- a/modules.json +++ b/modules.json @@ -122,7 +122,7 @@ }, "ribowaltz": { "branch": "master", - "git_sha": "5111d7a79aa8071bf2758cf64d6f5688879cc2be", + "git_sha": "b59f74e059a49fce82f19fbf684e2876da85ee39", "installed_by": ["modules"] }, "rsem/preparereference": { diff --git a/modules/local/ribowaltz_mqc/main.nf b/modules/local/ribowaltz_mqc/main.nf new file mode 100644 index 00000000..991d013d --- /dev/null +++ b/modules/local/ribowaltz_mqc/main.nf @@ -0,0 +1,31 @@ +process RIBOWALTZ_MQC { + tag "ribowaltz_mqc" + label 'process_single' + + conda "conda-forge::python=3.9" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.9' : + 'biocontainers/python:3.9' }" + + input: + path psite_region_files + path frames_files + path metaprofile_files + + output: + path "ribowaltz_psite_regions_mqc.tsv" , emit: psite_regions_mqc , optional: true + path "ribowaltz_frames_mqc.tsv" , emit: frames_mqc , optional: true + path "ribowaltz_metaprofile_start_mqc.json" , emit: metaprofile_start_mqc, optional: true + path "ribowaltz_metaprofile_stop_mqc.json" , emit: metaprofile_stop_mqc , optional: true + + when: + task.ext.when == null || task.ext.when + + script: + """ + ribowaltz_to_mqc.py psite_region ${psite_region_files} > ribowaltz_psite_regions_mqc.tsv + ribowaltz_to_mqc.py frames ${frames_files} > ribowaltz_frames_mqc.tsv + ribowaltz_to_mqc.py metaprofile_start ${metaprofile_files} > ribowaltz_metaprofile_start_mqc.json + ribowaltz_to_mqc.py metaprofile_stop ${metaprofile_files} > ribowaltz_metaprofile_stop_mqc.json + """ +} diff --git a/modules/nf-core/ribowaltz/main.nf b/modules/nf-core/ribowaltz/main.nf index e672c794..075d0478 100644 --- a/modules/nf-core/ribowaltz/main.nf +++ b/modules/nf-core/ribowaltz/main.nf @@ -22,6 +22,7 @@ process RIBOWALTZ { tuple val(meta), path("*.cds_coverage_psite.tsv{,.gz}") , emit: cds_coverage , optional: true tuple val(meta), path("*nt_coverage_psite.tsv{,.gz}") , emit: cds_window_coverage , optional: true tuple val(meta), path("ribowaltz_qc/*.pdf") , emit: ribowaltz_qc , optional: true + tuple val(meta), path("ribowaltz_qc/*.tsv") , emit: ribowaltz_qc_data , optional: true path "versions.yml" , emit: versions when: @@ -41,6 +42,9 @@ process RIBOWALTZ { touch ${prefix}.cds_coverage_psite.tsv mkdir -p offset_plot/${prefix} && touch offset_plot/${prefix}/29.pdf mkdir -p ribowaltz_qc && touch ribowaltz_qc/${prefix}.metaprofile_psite.pdf + touch ribowaltz_qc/${prefix}.psite_region.tsv + touch ribowaltz_qc/${prefix}.frames.tsv + touch ribowaltz_qc/${prefix}.frames_stratified.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ribowaltz/meta.yml b/modules/nf-core/ribowaltz/meta.yml index 14f85abd..e5a8f615 100644 --- a/modules/nf-core/ribowaltz/meta.yml +++ b/modules/nf-core/ribowaltz/meta.yml @@ -164,6 +164,21 @@ output: description: riboWaltz diagnostic plots (optional) pattern: "ribowaltz_qc/*" ontologies: [] + ribowaltz_qc_data: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ribowaltz_qc/*.tsv: + type: file + description: TSV files containing data underlying riboWaltz QC plots including + read length distribution, read length bins for P-site offset identification, + ends heatmap, codon usage, P-site region distribution, frame distribution, + frame distribution stratified by read length, and metaprofile P-site + frequency around start/stop codons (optional) + pattern: "ribowaltz_qc/*.tsv" + ontologies: [] versions: - versions.yml: type: file diff --git a/modules/nf-core/ribowaltz/templates/ribowaltz.r b/modules/nf-core/ribowaltz/templates/ribowaltz.r index c13c987f..b4a1d855 100644 --- a/modules/nf-core/ribowaltz/templates/ribowaltz.r +++ b/modules/nf-core/ribowaltz/templates/ribowaltz.r @@ -156,6 +156,11 @@ plot_length_bins <- function(sample_name, df_list) { ggplot2::ggsave(paste0(getwd(),"/ribowaltz_qc/", sample_name, ".length_bins_for_psite.pdf"), length_dist_split.gg, dpi = 400, width = 10, height = 5) + # Export underlying data + length_bins_dt <- length_dist_split[["count_dt"]] + if (!is.null(length_bins_dt)) { + data.table::fwrite(length_bins_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".length_bins_for_psite.tsv"), sep = "\t") + } } #' Export meta-heatmaps of read extremities around start and stop codons produced by the `riboWaltz::rends_heat` function @@ -176,6 +181,11 @@ plot_metaheatmap <- function(sample_name, df_list, annotation) { ggplot2::ggsave(paste0(getwd(),"/ribowaltz_qc/", sample_name, ".ends_heatmap.pdf"), ends_heatmap.gg, dpi = 400, width = 12, height = 8) + # Export underlying data + ends_heatmap_dt <- ends_heatmap[["count_dt"]] + if (!is.null(ends_heatmap_dt)) { + data.table::fwrite(ends_heatmap_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".ends_heatmap.tsv"), sep = "\t") + } } #' Export meta-heatmaps of read extremities around start and stop codons produced by the `riboWaltz::codon_usage_psite` function @@ -201,6 +211,12 @@ plot_codon_usage <- function(sample_name, psite_info_ls, frequency_normalization cu_barplot.gg <-cu_barplot[[paste0("plot_", sample_name)]] ggplot2::ggsave(paste0(getwd(),"/ribowaltz_qc/", sample_name, ".codon_usage.pdf"), cu_barplot.gg, dpi = 400, width = 10, height = 7) + + # Export underlying data + codon_usage_dt <- cu_barplot[["count_dt"]] + if (!is.null(codon_usage_dt)) { + data.table::fwrite(codon_usage_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".codon_usage.tsv"), sep = "\t") + } } @@ -268,6 +284,11 @@ save_length_distribution_plot <- function(sample_name, dt.ls) { ggplot2::ggsave(paste0(getwd(), "/ribowaltz_qc/", sample_name, ".length_distribution.pdf"), length_dist.gg, dpi = 400) + # Export underlying data + length_dist_dt <- length_dist[["count_dt"]] + if (!is.null(length_dist_dt)) { + data.table::fwrite(length_dist_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".length_distribution.tsv"), sep = "\t") + } } #' Save P-site Region Plot @@ -294,6 +315,11 @@ save_psite_region_plot <- function(sample_name, dt.ls, annotation.df) { ggplot2::ggsave(paste0(getwd(), "/ribowaltz_qc/", sample_name, ".psite_region.pdf"), psite_region.gg, dpi = 400, width = 10) + # Export underlying data + region_dt <- psite_region[["count_dt"]] + if (!is.null(region_dt)) { + data.table::fwrite(region_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".psite_region.tsv"), sep = "\t") + } } #' Save Frame Plots @@ -329,12 +355,22 @@ save_frame_plots <- function(sample_name, dt.ls, annotation.df, min_length, max_ ggplot2::ggsave(paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames_stratified.pdf"), frames_stratified.gg, dpi = 600, height = 9 , width = 12) + # Export underlying data for stratified frames + frames_stratified_dt <- frames_stratified[["count_dt"]] + if (!is.null(frames_stratified_dt)) { + data.table::fwrite(frames_stratified_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames_stratified.tsv"), sep = "\t") + } frames <- riboWaltz::frame_psite(dt.ls, region = "all", length_range = min_length:max_length, sample = sample_name, annotation = annotation.df, colour = "grey70") frames.gg <- frames[[paste0("plot_", sample_name)]] ggplot2::ggsave(paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames.pdf"), frames.gg, dpi = 600, height = 9 , width = 9) + # Export underlying data for aggregated frames + frames_dt <- frames[["count_dt"]] + if (!is.null(frames_dt)) { + data.table::fwrite(frames_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames.tsv"), sep = "\t") + } } @@ -368,6 +404,12 @@ save_metaprofile_psite_plot <- function(sample_name, df.ls, annotation.df) { ggplot2::ggsave(paste0(getwd(),"/ribowaltz_qc/", sample_name, ".metaprofile_psite.pdf"), metaprofiles.gg, dpi = 400, width = 12, height = 6) # save in wide format + # Export plot data for MultiQC + plot_dt <- metaprofile[["plot_dt"]] + if (!is.null(plot_dt)) { + write.table(plot_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".metaprofile_psite.tsv"), + sep = "\t", row.names = FALSE, quote = FALSE) + } } # ========= # Parse parameters for Nextflow diff --git a/modules/nf-core/ribowaltz/tests/main.nf.test b/modules/nf-core/ribowaltz/tests/main.nf.test index ace571ca..ed1af605 100644 --- a/modules/nf-core/ribowaltz/tests/main.nf.test +++ b/modules/nf-core/ribowaltz/tests/main.nf.test @@ -36,6 +36,7 @@ nextflow_process { { assert snapshot(process.out.cds_coverage).match('cds_coverage') }, { assert snapshot(process.out.cds_window_coverage).match('cds_window_coverage') }, { assert snapshot(process.out.ribowaltz_qc.size() == 8) }, + { assert snapshot(process.out.ribowaltz_qc_data.size() == 8) }, { assert snapshot(process.out.versions).match('versions') } ) } @@ -69,6 +70,7 @@ nextflow_process { { assert snapshot(process.out.codon_coverage_psite).match('codon_coverage_psite_stub') }, { assert snapshot(process.out.cds_coverage).match('cds_coverage_stub') }, { assert snapshot(process.out.ribowaltz_qc.size() == 1) }, + { assert snapshot(process.out.ribowaltz_qc_data.size() == 3) }, { assert snapshot(process.out.versions).match('versions_stub') } ) } diff --git a/subworkflows/local/ribowaltz_qc/main.nf b/subworkflows/local/ribowaltz_qc/main.nf new file mode 100644 index 00000000..10cb1c2b --- /dev/null +++ b/subworkflows/local/ribowaltz_qc/main.nf @@ -0,0 +1,72 @@ +// +// Run riboWaltz P-site analysis and prepare MultiQC outputs +// + +include { RIBOWALTZ } from '../../../modules/nf-core/ribowaltz/main' +include { RIBOWALTZ_MQC } from '../../../modules/local/ribowaltz_mqc/main' + +workflow RIBOWALTZ_QC { + take: + ch_transcriptome_bam // channel: [ val(meta), path(bam) ] + ch_gtf // channel: [ val(meta), path(gtf) ] + ch_fasta // channel: [ val(meta), path(fasta) ] + + main: + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() + + // + // MODULE: Run riboWaltz for P-site offset calculation and QC + // + RIBOWALTZ( + ch_transcriptome_bam, + ch_gtf, + ch_fasta + ) + ch_versions = ch_versions.mix(RIBOWALTZ.out.versions) + + // + // Prepare ribowaltz QC data for MultiQC custom content + // + ch_ribowaltz_psite_region = RIBOWALTZ.out.ribowaltz_qc_data + .map { meta, files -> files } + .flatten() + .filter { it.name.endsWith('.psite_region.tsv') } + .collect() + + ch_ribowaltz_frames = RIBOWALTZ.out.ribowaltz_qc_data + .map { meta, files -> files } + .flatten() + .filter { it.name.endsWith('.frames.tsv') && !it.name.contains('stratified') } + .collect() + + ch_ribowaltz_metaprofile = RIBOWALTZ.out.ribowaltz_qc_data + .map { meta, files -> files } + .flatten() + .filter { it.name.endsWith('.metaprofile_psite.tsv') } + .collect() + + // + // MODULE: Transform riboWaltz outputs to MultiQC custom content format + // + RIBOWALTZ_MQC( + ch_ribowaltz_psite_region, + ch_ribowaltz_frames, + ch_ribowaltz_metaprofile + ) + + ch_multiqc_files = ch_multiqc_files + .mix(RIBOWALTZ_MQC.out.psite_regions_mqc.ifEmpty([])) + .mix(RIBOWALTZ_MQC.out.frames_mqc.ifEmpty([])) + .mix(RIBOWALTZ_MQC.out.metaprofile_start_mqc.ifEmpty([])) + .mix(RIBOWALTZ_MQC.out.metaprofile_stop_mqc.ifEmpty([])) + + emit: + offset = RIBOWALTZ.out.offset // channel: [ val(meta), path(offset) ] + best_offset = RIBOWALTZ.out.best_offset // channel: [ val(meta), path(best_offset) ] + psites = RIBOWALTZ.out.psites // channel: [ val(meta), path(psites) ] + qc_plots = RIBOWALTZ.out.ribowaltz_qc // channel: [ val(meta), path(plots) ] + qc_data = RIBOWALTZ.out.ribowaltz_qc_data // channel: [ val(meta), path(data) ] + multiqc_files = ch_multiqc_files // channel: [ path(mqc_files) ] + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/workflows/riboseq/main.nf b/workflows/riboseq/main.nf index f54c1bc9..8f34a9c5 100644 --- a/workflows/riboseq/main.nf +++ b/workflows/riboseq/main.nf @@ -35,7 +35,7 @@ include { RIBOTRICER_DETECTORFS } from '../../mod include { ANOTA2SEQ_ANOTA2SEQRUN } from '../../modules/nf-core/anota2seq/anota2seqrun' include { DESEQ2_DELTATE } from '../../modules/local/deseq2/deltate' include { QUANTIFY_PSEUDO_ALIGNMENT as QUANTIFY_STAR_SALMON } from '../../subworkflows/nf-core/quantify_pseudo_alignment' -include { RIBOWALTZ } from '../../modules/nf-core/ribowaltz/main' +include { RIBOWALTZ_QC } from '../../subworkflows/local/ribowaltz_qc/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -338,13 +338,17 @@ workflow RIBOSEQ { } .set { ch_transcriptome_bam_by_type } + // + // SUBWORKFLOW: Run riboWaltz P-site analysis and prepare MultiQC outputs + // if (!params.skip_ribowaltz) { - RIBOWALTZ( + RIBOWALTZ_QC( ch_transcriptome_bam_by_type.riboseq, ch_gtf.map { [ [:], it ] }, - ch_fasta.map { [ [:], it ] }) - - ch_versions = ch_versions.mix(RIBOWALTZ.out.versions) + ch_fasta.map { [ [:], it ] } + ) + ch_versions = ch_versions.mix(RIBOWALTZ_QC.out.versions) + ch_multiqc_files = ch_multiqc_files.mix(RIBOWALTZ_QC.out.multiqc_files) } // From b458d6ec6633ba1f9c3c9052e5114c29520ad5ea Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Dec 2025 17:44:40 +0000 Subject: [PATCH 02/11] order tweak --- assets/multiqc_config.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 594c349a..d9754863 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -48,7 +48,6 @@ top_modules: - "fail_trimmed_samples" - "fail_mapped_samples" - "fail_strand_check" - - "ribowaltz" - "star_rsem_deseq2_pca" - "star_rsem_deseq2_clustering" - "star_salmon_deseq2_pca" @@ -56,6 +55,7 @@ top_modules: - "salmon_deseq2_pca" - "salmon_deseq2_clustering" - "biotype_counts" + - "ribowaltz" - "dupradar" module_order: @@ -83,6 +83,7 @@ module_order: - "*_trimmed_fastqc.zip" - star - samtools + - ribowaltz - ribotish # Don't show % Dups in the General Stats table (we have this from Picard) From bc54beb5cada0f696980d113061971b8ff63dddf Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Dec 2025 17:53:42 +0000 Subject: [PATCH 03/11] fix: Use report_section_order for MultiQC section ordering Replace top_modules with numeric report_section_order to properly control the position of riboWaltz and other custom content sections in the MultiQC report. --- assets/multiqc_config.yml | 44 ++++++++++++++++++++++++++------------- 1 file changed, 29 insertions(+), 15 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d9754863..f9f168d0 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,6 +1,35 @@ report_comment: > This report has been generated by the nf-core/riboseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: + # Important checks and failures + fail_trimmed_samples-module: + order: 5003 + fail_mapped_samples-module: + order: 5002 + fail_strand_check-module: + order: 5001 + # Post-alignment QC + samtools: + order: 3000 + # Ribo-seq specific QC + ribowaltz: + order: 2500 + ribotish: + order: 2500 + # Post-quantification QC + star_rsem_deseq2_pca: + order: 1005 + star_rsem_deseq2_clustering: + order: 1004 + star_salmon_deseq2_pca: + order: 1003 + star_salmon_deseq2_clustering: + order: 1002 + salmon_deseq2_pca: + order: 1001 + salmon_deseq2_clustering: + order: 1000 + # Summaries "nf-core-riboseq-methods-description": order: -1000 software_versions: @@ -43,21 +72,6 @@ run_modules: - qualimap - ribotish -# Order of modules -top_modules: - - "fail_trimmed_samples" - - "fail_mapped_samples" - - "fail_strand_check" - - "star_rsem_deseq2_pca" - - "star_rsem_deseq2_clustering" - - "star_salmon_deseq2_pca" - - "star_salmon_deseq2_clustering" - - "salmon_deseq2_pca" - - "salmon_deseq2_clustering" - - "biotype_counts" - - "ribowaltz" - - "dupradar" - module_order: - fastqc: name: "FastQC (raw)" From 518dfb5c009f50649d630b2efb335de7e331c5a2 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Dec 2025 17:57:23 +0000 Subject: [PATCH 04/11] fix: Add ordering for all MultiQC sections Add report_section_order entries for preprocessing, alignment, and post-alignment QC sections so riboWaltz appears in the correct position (after alignment stats, before downstream analysis). --- assets/multiqc_config.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f9f168d0..ad25001f 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -8,9 +8,31 @@ report_section_order: order: 5002 fail_strand_check-module: order: 5001 + # Preprocessing and pre-alignment QC + fastqc_raw: + order: 4004 + cutadapt: + order: 4003 + fastp: + order: 4003 + fastqc_trimmed: + order: 4002 + sortmerna: + order: 4001 + # Alignment + star: + order: 3001 + hisat2: + order: 3001 # Post-alignment QC samtools: order: 3000 + picard: + order: 3000 + rseqc: + order: 3000 + qualimap: + order: 3000 # Ribo-seq specific QC ribowaltz: order: 2500 From c0e21c80d35cbf4711e09f2949b4c20cc828454a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Dec 2025 18:01:43 +0000 Subject: [PATCH 05/11] fix: Add anchors for FastQC sections in module_order Add anchor properties to FastQC entries so they can be referenced by fastqc_raw and fastqc_trimmed in report_section_order. --- assets/multiqc_config.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ad25001f..80b782ff 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -96,6 +96,7 @@ run_modules: module_order: - fastqc: + anchor: "fastqc_raw" name: "FastQC (raw)" info: "This section of the report shows FastQC results before adapter trimming." path_filters: @@ -113,6 +114,7 @@ module_order: path_filters: - "*.riboseq_readlength_stats.tsv" - fastqc: + anchor: "fastqc_trimmed" name: "FastQC (trimmed)" info: "This section of the report shows FastQC results after adapter trimming." path_filters: From 582fb6f00025383dd46af3819842831d41a0392f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Dec 2025 18:05:23 +0000 Subject: [PATCH 06/11] docs: Add changelog entry for PR #139 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0722a9af..8ed3397e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#128](https://github.com/nf-core/riboseq/pull/128) - Add DESeq2-based deltaTE analysis as an alternative to anota2seq for translational efficiency analysis ([@pinin4fjords](https://github.com/pinin4fjords)) - [#131](https://github.com/nf-core/riboseq/pull/131) - Add ribotish quality output routing to MultiQC ([@pinin4fjords](https://github.com/pinin4fjords)) - [#135](https://github.com/nf-core/riboseq/pull/135) - Add optional read length equalisation to trim RNA-seq reads to match Ribo-seq lengths before quantification ([@pinin4fjords](https://github.com/pinin4fjords)) +- [#139](https://github.com/nf-core/riboseq/pull/139) - Add riboWaltz QC plots to MultiQC report (P-site regions, reading frames, metaprofiles) ([@pinin4fjords](https://github.com/pinin4fjords)) ### `Fixed` From 4687b425dbb79bc6145cac980c66682c5ea87b17 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 5 Jan 2026 12:07:15 +0000 Subject: [PATCH 07/11] refactor: Use branch operator for riboWaltz QC channel splitting MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Simplify channel operations by using a single branch operator instead of three separate map/flatten/filter chains. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 --- subworkflows/local/ribowaltz_qc/main.nf | 28 +++++++++---------------- 1 file changed, 10 insertions(+), 18 deletions(-) diff --git a/subworkflows/local/ribowaltz_qc/main.nf b/subworkflows/local/ribowaltz_qc/main.nf index 10cb1c2b..3e25a172 100644 --- a/subworkflows/local/ribowaltz_qc/main.nf +++ b/subworkflows/local/ribowaltz_qc/main.nf @@ -28,31 +28,23 @@ workflow RIBOWALTZ_QC { // // Prepare ribowaltz QC data for MultiQC custom content // - ch_ribowaltz_psite_region = RIBOWALTZ.out.ribowaltz_qc_data + RIBOWALTZ.out.ribowaltz_qc_data .map { meta, files -> files } .flatten() - .filter { it.name.endsWith('.psite_region.tsv') } - .collect() - - ch_ribowaltz_frames = RIBOWALTZ.out.ribowaltz_qc_data - .map { meta, files -> files } - .flatten() - .filter { it.name.endsWith('.frames.tsv') && !it.name.contains('stratified') } - .collect() - - ch_ribowaltz_metaprofile = RIBOWALTZ.out.ribowaltz_qc_data - .map { meta, files -> files } - .flatten() - .filter { it.name.endsWith('.metaprofile_psite.tsv') } - .collect() + .branch { file -> + psite_region: file.name.endsWith('.psite_region.tsv') + frames: file.name.endsWith('.frames.tsv') && !file.name.contains('stratified') + metaprofile: file.name.endsWith('.metaprofile_psite.tsv') + } + .set { ch_ribowaltz_qc } // // MODULE: Transform riboWaltz outputs to MultiQC custom content format // RIBOWALTZ_MQC( - ch_ribowaltz_psite_region, - ch_ribowaltz_frames, - ch_ribowaltz_metaprofile + ch_ribowaltz_qc.psite_region.collect(), + ch_ribowaltz_qc.frames.collect(), + ch_ribowaltz_qc.metaprofile.collect() ) ch_multiqc_files = ch_multiqc_files From c3cddf9353773a0cb82f51abbfaaf000aa14e04f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 5 Jan 2026 12:29:05 +0000 Subject: [PATCH 08/11] refactor: Simplify ribowaltz_to_mqc.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Extract common constants (PARENT_ID, PARENT_NAME, PARENT_DESC, REGIONS) - Add read_tsv_files() generator for DRY file reading - Add print_bargraph_header() helper for repeated YAML output - Simplify transform_metaprofile() using string formatting - Use dispatch dict instead of if/elif chain 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 --- bin/ribowaltz_to_mqc.py | 232 +++++++++++++++------------------------- 1 file changed, 88 insertions(+), 144 deletions(-) diff --git a/bin/ribowaltz_to_mqc.py b/bin/ribowaltz_to_mqc.py index bbd2284d..3668b32f 100755 --- a/bin/ribowaltz_to_mqc.py +++ b/bin/ribowaltz_to_mqc.py @@ -14,194 +14,139 @@ import json from collections import defaultdict +# Common constants +PARENT_ID = "ribowaltz" +PARENT_NAME = "riboWaltz" +PARENT_DESC = 'Quality control metrics from riboWaltz for assessing Ribo-seq data quality.' -def transform_psite_region(files): - """Transform psite_region.tsv files to wide format for MultiQC bargraph.""" - data = defaultdict(dict) - rna_ref = {} # Global RNA-seq reference from annotation - regions = ["5' UTR", "CDS", "3' UTR"] +REGIONS = ["5' UTR", "CDS", "3' UTR"] +REGION_MAP = {"5' UTR": "5' UTR", "5utr": "5' UTR", "CDS": "CDS", "cds": "CDS", "3' UTR": "3' UTR", "3utr": "3' UTR"} - region_map = {"5' UTR": "5' UTR", "5utr": "5' UTR", - "CDS": "CDS", "cds": "CDS", - "3' UTR": "3' UTR", "3utr": "3' UTR"} +def read_tsv_files(files): + """Yield rows from multiple TSV files.""" for filepath in files: with open(filepath, 'r') as f: - reader = csv.DictReader(f, delimiter='\t') - for row in reader: - sample = row['sample'] - region = row['region'] - clean_region = region_map.get(region, region) + yield from csv.DictReader(f, delimiter='\t') - # Capture the 'RNAs' reference (same for all samples using same annotation) - if sample == 'RNAs': - if clean_region in regions and clean_region not in rna_ref: - rna_ref[clean_region] = float(row['scaled_count']) - continue - if clean_region in regions: - data[sample][clean_region] = float(row['scaled_count']) - - samples = sorted(data.keys()) - - # Output YAML header - print("# id: 'ribowaltz_1_psite_regions'") - print("# section_name: 'P-site Region Distribution'") - print("# description: 'Distribution of P-sites across transcript regions. Good Ribo-seq data shows strong CDS enrichment (>70%). The RNA-seq reference shows expected distribution from uniform transcript coverage.'") - print("# parent_id: 'ribowaltz'") - print("# parent_name: 'riboWaltz'") - print("# parent_description: 'Quality control metrics from riboWaltz for assessing Ribo-seq data quality.'") +def print_bargraph_header(plot_id, section_name, description, ylab="% of P-sites"): + """Print common YAML header for bargraph plots.""" + print(f"# id: '{plot_id}'") + print(f"# section_name: '{section_name}'") + print(f"# description: '{description}'") + print(f"# parent_id: '{PARENT_ID}'") + print(f"# parent_name: '{PARENT_NAME}'") + print(f"# parent_description: '{PARENT_DESC}'") print("# plot_type: 'bargraph'") print("# pconfig:") - print("# id: 'ribowaltz_1_psite_regions_plot'") - print("# title: 'riboWaltz: P-site Region Distribution'") - print("# ylab: '% of P-sites'") + print(f"# id: '{plot_id}_plot'") + print(f"# title: '{PARENT_NAME}: {section_name}'") + print(f"# ylab: '{ylab}'") print("# cpswitch: false") - # Output data - print("Sample\t" + "\t".join(regions)) - # Output RNA-seq reference first if available +def transform_psite_region(files): + """Transform psite_region.tsv files to wide format for MultiQC bargraph.""" + data = defaultdict(dict) + rna_ref = {} + + for row in read_tsv_files(files): + sample = row['sample'] + region = REGION_MAP.get(row['region'], row['region']) + + if sample == 'RNAs': + if region in REGIONS and region not in rna_ref: + rna_ref[region] = float(row['scaled_count']) + elif region in REGIONS: + data[sample][region] = float(row['scaled_count']) + + print_bargraph_header( + "ribowaltz_1_psite_regions", + "P-site Region Distribution", + "Distribution of P-sites across transcript regions. Good Ribo-seq data shows strong CDS enrichment (>70%). The RNA-seq reference shows expected distribution from uniform transcript coverage." + ) + + print("Sample\t" + "\t".join(REGIONS)) if rna_ref: - values = [str(round(rna_ref.get(r, 0), 1)) for r in regions] + values = [str(round(rna_ref.get(r, 0), 1)) for r in REGIONS] print(f"RNA-seq reference\t" + "\t".join(values)) - - for sample in samples: - values = [str(round(data[sample].get(r, 0), 1)) for r in regions] + for sample in sorted(data.keys()): + values = [str(round(data[sample].get(r, 0), 1)) for r in REGIONS] print(f"{sample}\t" + "\t".join(values)) def transform_frames(files): - """Transform frames.tsv files to MultiQC custom content. - - Structure matches ribowaltz frames.pdf plot: - - Groups: regions (5' UTR, CDS, 3' UTR) - using sample_groups - - Within each group: one bar per sample - - Each bar stacked: Frame 0, Frame 1, Frame 2 segments - - Key QC insight: CDS should show Frame 0 enrichment, UTRs should not. - """ + """Transform frames.tsv files to MultiQC custom content.""" data = defaultdict(lambda: defaultdict(dict)) frames = ["Frame 0", "Frame 1", "Frame 2"] - regions = ["5utr", "cds", "3utr"] + region_keys = ["5utr", "cds", "3utr"] region_labels = {"5utr": "5' UTR", "cds": "CDS", "3utr": "3' UTR"} + to_key = {"5' UTR": "5utr", "5utr": "5utr", "CDS": "cds", "cds": "cds", "3' UTR": "3utr", "3utr": "3utr"} - region_map = { - "5' UTR": "5utr", "5utr": "5utr", - "CDS": "cds", "cds": "cds", - "3' UTR": "3utr", "3utr": "3utr" - } - - for filepath in files: - with open(filepath, 'r') as f: - reader = csv.DictReader(f, delimiter='\t') - for row in reader: - sample = row['sample'] - region = region_map.get(row['region'], row['region']) - frame = f"Frame {row['frame']}" - if region in regions and frame in frames: - data[sample][region][frame] = float(row['scaled_count']) + for row in read_tsv_files(files): + sample = row['sample'] + region = to_key.get(row['region'], row['region']) + frame = f"Frame {row['frame']}" + if region in region_keys and frame in frames: + data[sample][region][frame] = float(row['scaled_count']) samples = sorted(data.keys()) - # Output YAML header - print("# id: 'ribowaltz_2_frames'") - print("# section_name: 'Reading Frame Distribution'") - print("# description: 'Distribution of P-sites across reading frames for each transcript region. Good Ribo-seq data shows Frame 0 enrichment (>50%) in the CDS but not in UTRs.'") - print("# parent_id: 'ribowaltz'") - print("# parent_name: 'riboWaltz'") - print("# parent_description: 'Quality control metrics from riboWaltz for assessing Ribo-seq data quality.'") - print("# plot_type: 'bargraph'") - print("# pconfig:") - print("# id: 'ribowaltz_2_frames_plot'") - print("# title: 'riboWaltz: Reading Frame Distribution'") - print("# ylab: '% of P-sites'") - print("# cpswitch: false") + print_bargraph_header( + "ribowaltz_2_frames", + "Reading Frame Distribution", + "Distribution of P-sites across reading frames for each transcript region. Good Ribo-seq data shows Frame 0 enrichment (>50%) in the CDS but not in UTRs." + ) - # Build sample_groups: group by region, with samples within each region group - # Structure: {"5' UTR": [["sample1_5' UTR", "sample1"], ...], "CDS": [...], ...} - if len(samples) > 0: + if samples: print("# sample_groups:") - for region in regions: + for region in region_keys: label = region_labels[region] print(f'# "{label}":') for sample in samples: - # [sample_key, display_label] - display_label is the sample name print(f'# - ["{sample}_{label}", "{sample}"]') - # Output data: each row is {sample}_{region} with frame values print("Sample\t" + "\t".join(frames)) for sample in samples: - for region in regions: + for region in region_keys: label = region_labels[region] - row_id = f"{sample}_{label}" values = [str(round(data[sample][region].get(f, 0), 1)) for f in frames] - print(f"{row_id}\t" + "\t".join(values)) + print(f"{sample}_{label}\t" + "\t".join(values)) def transform_metaprofile(files, region_filter): - """Transform metaprofile_psite.tsv files to MultiQC linegraph JSON format. - - Args: - files: List of metaprofile TSV files - region_filter: "start" or "stop" to filter by region type - - The input TSV has columns: sample, region, x, y - Region values are "Distance from start (nt)" or "Distance from stop (nt)" - """ + """Transform metaprofile_psite.tsv files to MultiQC linegraph JSON format.""" data = defaultdict(list) + target_region = f"Distance from {region_filter} (nt)" - region_map = { - "start": "Distance from start (nt)", - "stop": "Distance from stop (nt)" - } - target_region = region_map[region_filter] + for row in read_tsv_files(files): + if row['region'] == target_region: + data[row['sample']].append([int(float(row['x'])), round(float(row['y']), 2)]) - for filepath in files: - with open(filepath, 'r') as f: - reader = csv.DictReader(f, delimiter='\t') - for row in reader: - sample = row['sample'] - region = row['region'] - if region == target_region: - x = int(float(row['x'])) - y = round(float(row['y']), 2) - data[sample].append([x, y]) - - # Sort each sample's data by x value for sample in data: - data[sample].sort(key=lambda point: point[0]) - - # Build JSON output - if region_filter == "start": - section_name = "Metaprofile (Start Codon)" - description = "P-site frequency around the start codon. Good Ribo-seq data shows trinucleotide periodicity with peaks at frame 0 positions." - plot_id = "ribowaltz_3_metaprofile_start" - xlab = "Distance from start codon (nt)" - else: - section_name = "Metaprofile (Stop Codon)" - description = "P-site frequency around the stop codon. Good Ribo-seq data shows trinucleotide periodicity with peaks at frame 0 positions." - plot_id = "ribowaltz_4_metaprofile_stop" - xlab = "Distance from stop codon (nt)" + data[sample].sort(key=lambda p: p[0]) + + section_name = f"Metaprofile ({region_filter.title()} Codon)" + plot_id = f"ribowaltz_{'3' if region_filter == 'start' else '4'}_metaprofile_{region_filter}" output = { "id": plot_id, "section_name": section_name, - "description": description, - "parent_id": "ribowaltz", - "parent_name": "riboWaltz", - "parent_description": "Quality control metrics from riboWaltz for assessing Ribo-seq data quality.", + "description": f"P-site frequency around the {region_filter} codon. Good Ribo-seq data shows trinucleotide periodicity with peaks at frame 0 positions.", + "parent_id": PARENT_ID, + "parent_name": PARENT_NAME, + "parent_description": PARENT_DESC, "plot_type": "linegraph", "pconfig": { "id": f"{plot_id}_plot", - "title": f"riboWaltz: {section_name}", - "xlab": xlab, + "title": f"{PARENT_NAME}: {section_name}", + "xlab": f"Distance from {region_filter} codon (nt)", "ylab": "P-site frequency", "x_decimals": False }, "data": dict(sorted(data.items())) } - print(json.dumps(output, indent=2)) @@ -210,17 +155,16 @@ def transform_metaprofile(files, region_filter): print(__doc__, file=sys.stderr) sys.exit(1) - mode = sys.argv[1] - files = sys.argv[2:] - - if mode == "psite_region": - transform_psite_region(files) - elif mode == "frames": - transform_frames(files) - elif mode == "metaprofile_start": - transform_metaprofile(files, "start") - elif mode == "metaprofile_stop": - transform_metaprofile(files, "stop") + mode, files = sys.argv[1], sys.argv[2:] + modes = { + "psite_region": lambda: transform_psite_region(files), + "frames": lambda: transform_frames(files), + "metaprofile_start": lambda: transform_metaprofile(files, "start"), + "metaprofile_stop": lambda: transform_metaprofile(files, "stop"), + } + + if mode in modes: + modes[mode]() else: print(f"Unknown mode: {mode}", file=sys.stderr) print(__doc__, file=sys.stderr) From 67f181994b4935e99a5e3fc35755d72c0327f9ad Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 5 Jan 2026 13:36:19 +0000 Subject: [PATCH 09/11] Update snaps --- tests/default.nf.test.snap | 890 ++++++++++++++-------- tests/deltate.nf.test.snap | 908 +++++++++++++++-------- tests/equalise_read_lengths.nf.test.snap | 908 +++++++++++++++-------- tests/ribo_removal_bowtie2.nf.test.snap | 908 +++++++++++++++-------- 4 files changed, 2330 insertions(+), 1284 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8b8a507f..77eff776 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -307,37 +307,41 @@ "multiqc/star/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star/multiqc_report_data/fastqc-1-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc-1_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_duplication_levels_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_top_overrepresented_sequences_table.txt", - "multiqc/star/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/llms-full.txt", "multiqc/star/multiqc_report_data/multiqc.log", "multiqc/star/multiqc_report_data/multiqc.parquet", "multiqc/star/multiqc_report_data/multiqc_citations.txt", "multiqc/star/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star/multiqc_report_data/multiqc_data.json", - "multiqc/star/multiqc_report_data/multiqc_fastqc.txt", - "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc-1.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", "multiqc/star/multiqc_report_data/multiqc_general_stats.txt", "multiqc/star/multiqc_report_data/multiqc_ribotish.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_1_psite_regions_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_2_frames_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_3_metaprofile_start_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_4_metaprofile_stop_plot.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_stats.txt", @@ -363,31 +367,35 @@ "multiqc/star/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_duplication_levels_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_top_overrepresented_sequences_table.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_frame_proportions.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_read_length_line.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_1_psite_regions_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_2_frames_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_3_metaprofile_start_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_4_metaprofile_stop_plot.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -409,31 +417,35 @@ "multiqc/star/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_duplication_levels_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_top_overrepresented_sequences_table.png", - "multiqc/star/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/ribotish_frame_proportions.png", "multiqc/star/multiqc_report_plots/png/ribotish_read_length_line.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_1_psite_regions_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_2_frames_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_3_metaprofile_start_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_4_metaprofile_stop_plot.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-pct-table.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-table.png", "multiqc/star/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -455,31 +467,35 @@ "multiqc/star/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_duplication_levels_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_top_overrepresented_sequences_table.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_frame_proportions.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_read_length_line.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_1_psite_regions_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_2_frames_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_3_metaprofile_start_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_4_metaprofile_stop_plot.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -520,6 +536,32 @@ "orf_predictions/ribotish_all/allsamples_all.txt", "orf_predictions/ribotish_all/allsamples_pred.txt", "orf_predictions/ribotish_all/allsamples_transprofile.py", + "other", + "other/ribowaltz", + "other/ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780885.psite.tsv.gz", + "other/ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780886.psite.tsv.gz", + "other/ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780887.psite.tsv.gz", + "other/ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780888.psite.tsv.gz", + "other/ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780889.psite.tsv.gz", + "other/ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780890.psite.tsv.gz", "pipeline_info", "pipeline_info/nf_core_riboseq_software_mqc_versions.yml", "preprocessing", @@ -882,188 +924,211 @@ "riboseq_qc/ribotish/SRX11780890.para.py", "riboseq_qc/ribotish/SRX11780890_qual.pdf", "riboseq_qc/ribotish/SRX11780890_qual.txt", + "riboseq_qc/ribowaltz", + "riboseq_qc/ribowaltz/SRX11780885.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780885.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780886.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780886.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780887.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780887.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780888.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780888.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780889.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780889.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780890.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780890.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/offset_plot", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/35.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/36.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/37.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/38.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/39.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/40.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/41.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/33.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.tsv", "ribowaltz", - "ribowaltz/SRX11780885.best_offset.txt", - "ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780885.psite.tsv.gz", - "ribowaltz/SRX11780885.psite_offset.tsv.gz", - "ribowaltz/SRX11780886.best_offset.txt", - "ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780886.psite.tsv.gz", - "ribowaltz/SRX11780886.psite_offset.tsv.gz", - "ribowaltz/SRX11780887.best_offset.txt", - "ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780887.psite.tsv.gz", - "ribowaltz/SRX11780887.psite_offset.tsv.gz", - "ribowaltz/SRX11780888.best_offset.txt", - "ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780888.psite.tsv.gz", - "ribowaltz/SRX11780888.psite_offset.tsv.gz", - "ribowaltz/SRX11780889.best_offset.txt", - "ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780889.psite.tsv.gz", - "ribowaltz/SRX11780889.psite_offset.tsv.gz", - "ribowaltz/SRX11780890.best_offset.txt", - "ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780890.psite.tsv.gz", - "ribowaltz/SRX11780890.psite_offset.tsv.gz", - "ribowaltz/offset_plot", - "ribowaltz/offset_plot/SRX11780885", - "ribowaltz/offset_plot/SRX11780885/22.pdf", - "ribowaltz/offset_plot/SRX11780885/23.pdf", - "ribowaltz/offset_plot/SRX11780885/24.pdf", - "ribowaltz/offset_plot/SRX11780885/25.pdf", - "ribowaltz/offset_plot/SRX11780885/26.pdf", - "ribowaltz/offset_plot/SRX11780885/27.pdf", - "ribowaltz/offset_plot/SRX11780885/28.pdf", - "ribowaltz/offset_plot/SRX11780885/29.pdf", - "ribowaltz/offset_plot/SRX11780885/30.pdf", - "ribowaltz/offset_plot/SRX11780885/31.pdf", - "ribowaltz/offset_plot/SRX11780885/32.pdf", - "ribowaltz/offset_plot/SRX11780885/33.pdf", - "ribowaltz/offset_plot/SRX11780885/34.pdf", - "ribowaltz/offset_plot/SRX11780886", - "ribowaltz/offset_plot/SRX11780886/20.pdf", - "ribowaltz/offset_plot/SRX11780886/21.pdf", - "ribowaltz/offset_plot/SRX11780886/22.pdf", - "ribowaltz/offset_plot/SRX11780886/23.pdf", - "ribowaltz/offset_plot/SRX11780886/24.pdf", - "ribowaltz/offset_plot/SRX11780886/25.pdf", - "ribowaltz/offset_plot/SRX11780886/26.pdf", - "ribowaltz/offset_plot/SRX11780886/27.pdf", - "ribowaltz/offset_plot/SRX11780886/28.pdf", - "ribowaltz/offset_plot/SRX11780886/29.pdf", - "ribowaltz/offset_plot/SRX11780886/30.pdf", - "ribowaltz/offset_plot/SRX11780886/31.pdf", - "ribowaltz/offset_plot/SRX11780886/32.pdf", - "ribowaltz/offset_plot/SRX11780886/33.pdf", - "ribowaltz/offset_plot/SRX11780887", - "ribowaltz/offset_plot/SRX11780887/20.pdf", - "ribowaltz/offset_plot/SRX11780887/21.pdf", - "ribowaltz/offset_plot/SRX11780887/22.pdf", - "ribowaltz/offset_plot/SRX11780887/23.pdf", - "ribowaltz/offset_plot/SRX11780887/24.pdf", - "ribowaltz/offset_plot/SRX11780887/25.pdf", - "ribowaltz/offset_plot/SRX11780887/26.pdf", - "ribowaltz/offset_plot/SRX11780887/27.pdf", - "ribowaltz/offset_plot/SRX11780887/28.pdf", - "ribowaltz/offset_plot/SRX11780887/29.pdf", - "ribowaltz/offset_plot/SRX11780887/30.pdf", - "ribowaltz/offset_plot/SRX11780887/31.pdf", - "ribowaltz/offset_plot/SRX11780887/32.pdf", - "ribowaltz/offset_plot/SRX11780887/33.pdf", - "ribowaltz/offset_plot/SRX11780887/34.pdf", - "ribowaltz/offset_plot/SRX11780887/35.pdf", - "ribowaltz/offset_plot/SRX11780887/36.pdf", - "ribowaltz/offset_plot/SRX11780887/37.pdf", - "ribowaltz/offset_plot/SRX11780887/38.pdf", - "ribowaltz/offset_plot/SRX11780887/39.pdf", - "ribowaltz/offset_plot/SRX11780887/40.pdf", - "ribowaltz/offset_plot/SRX11780887/41.pdf", - "ribowaltz/offset_plot/SRX11780888", - "ribowaltz/offset_plot/SRX11780888/21.pdf", - "ribowaltz/offset_plot/SRX11780888/22.pdf", - "ribowaltz/offset_plot/SRX11780888/23.pdf", - "ribowaltz/offset_plot/SRX11780888/24.pdf", - "ribowaltz/offset_plot/SRX11780888/25.pdf", - "ribowaltz/offset_plot/SRX11780888/26.pdf", - "ribowaltz/offset_plot/SRX11780888/27.pdf", - "ribowaltz/offset_plot/SRX11780888/28.pdf", - "ribowaltz/offset_plot/SRX11780888/29.pdf", - "ribowaltz/offset_plot/SRX11780888/30.pdf", - "ribowaltz/offset_plot/SRX11780889", - "ribowaltz/offset_plot/SRX11780889/22.pdf", - "ribowaltz/offset_plot/SRX11780889/23.pdf", - "ribowaltz/offset_plot/SRX11780889/24.pdf", - "ribowaltz/offset_plot/SRX11780889/25.pdf", - "ribowaltz/offset_plot/SRX11780889/26.pdf", - "ribowaltz/offset_plot/SRX11780889/27.pdf", - "ribowaltz/offset_plot/SRX11780889/28.pdf", - "ribowaltz/offset_plot/SRX11780889/29.pdf", - "ribowaltz/offset_plot/SRX11780889/30.pdf", - "ribowaltz/offset_plot/SRX11780889/31.pdf", - "ribowaltz/offset_plot/SRX11780889/32.pdf", - "ribowaltz/offset_plot/SRX11780890", - "ribowaltz/offset_plot/SRX11780890/21.pdf", - "ribowaltz/offset_plot/SRX11780890/22.pdf", - "ribowaltz/offset_plot/SRX11780890/23.pdf", - "ribowaltz/offset_plot/SRX11780890/24.pdf", - "ribowaltz/offset_plot/SRX11780890/25.pdf", - "ribowaltz/offset_plot/SRX11780890/26.pdf", - "ribowaltz/offset_plot/SRX11780890/27.pdf", - "ribowaltz/offset_plot/SRX11780890/28.pdf", - "ribowaltz/offset_plot/SRX11780890/29.pdf", - "ribowaltz/offset_plot/SRX11780890/30.pdf", - "ribowaltz/offset_plot/SRX11780890/31.pdf", - "ribowaltz/offset_plot/SRX11780890/32.pdf", - "ribowaltz/offset_plot/SRX11780890/33.pdf", - "ribowaltz/ribowaltz_qc", - "ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "ribowaltz/ribowaltz_frames_mqc.tsv", + "ribowaltz/ribowaltz_metaprofile_start_mqc.json", + "ribowaltz/ribowaltz_metaprofile_stop_mqc.json", + "ribowaltz/ribowaltz_psite_regions_mqc.tsv", "translational_efficiency", "translational_efficiency/anota2seq", "translational_efficiency/anota2seq/treated_vs_control.Anota2seqDataSet.rds", @@ -1145,30 +1210,36 @@ "cutadapt_filtered_reads_plot.txt:md5,ff95c965185e62ff5914a5c60e7a268f", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,319e9bb90c170c4b0207d644926bf69a", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,6ed5bbd0961572352d1614cc1f25f29d", - "fastqc-1-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc-1_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", - "fastqc-1_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", - "fastqc-1_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", - "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", - "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", - "fastqc-1_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", - "fastqc-1_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", - "fastqc-1_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", - "fastqc-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", - "fastqc_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", - "fastqc_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", - "fastqc_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", - "fastqc_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", - "fastqc_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", + "fastqc_raw_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", + "fastqc_raw_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,cdd555433a5c5bae529cd086512cbb69", "fastqc_sequence_length_distribution_plot.txt:md5,d3f33f3eda7927b061fc3cdec99e8f4e", - "multiqc_citations.txt:md5,224ea957336bbafdbbeaa2bc047d04f8", + "fastqc_trimmed-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", + "fastqc_trimmed_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", + "fastqc_trimmed_top_overrepresented_sequences_table.txt:md5,18dd505c347a3faac767f31b740265d4", + "multiqc_citations.txt:md5,77699c5515552ac650db4a5fc89c8f3e", "multiqc_cutadapt.txt:md5,e6031ab468a23c95b6989a6ce9e081f5", - "multiqc_fastqc.txt:md5,435f987c78b50ab1dfe18640246f580b", - "multiqc_fastqc_fastqc-1.txt:md5,c8ce8940114de9321e6de124b6cb4c18", + "multiqc_fastqc_fastqc_raw.txt:md5,435f987c78b50ab1dfe18640246f580b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,c8ce8940114de9321e6de124b6cb4c18", "multiqc_ribotish.txt:md5,21546543970095b3bcc6ab20ac0425e7", + "multiqc_ribowaltz_1_psite_regions_plot.txt:md5,0a054c20541cee8a35a98e841d828837", + "multiqc_ribowaltz_2_frames_plot.txt:md5,2d3805092494ba14f3cba0d862c34656", + "multiqc_ribowaltz_3_metaprofile_start_plot.txt:md5,4d63cc9e6fbcdac63cb222eb1c2709a9", + "multiqc_ribowaltz_4_metaprofile_stop_plot.txt:md5,dedfc06570e87423138ddf8ca9bdc23e", "multiqc_samtools_flagstat.txt:md5,14e8d04345d9da81e5cc6cb049f5d396", "multiqc_samtools_idxstats.txt:md5,338c19030305e7c9293511f1d98828f7", "multiqc_samtools_stats.txt:md5,c51940af3e59e1ffac93b89f143f6026", @@ -1207,6 +1278,30 @@ "allsamples_all.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_pred.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_transprofile.py:md5,10add18b7c9d626042b8980ee896adb9", + "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", + "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", + "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", + "SRX11780885.psite.tsv.gz:md5,517cfb43200a4d77598e7cea3d654460", + "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", + "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", + "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", + "SRX11780886.psite.tsv.gz:md5,78de44e6dbda8f3914d52a068acde6bd", + "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", + "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", + "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", + "SRX11780887.psite.tsv.gz:md5,7e510dc502bdf00f58c165237683cead", + "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", + "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", + "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", + "SRX11780888.psite.tsv.gz:md5,f47672a5ec625ad56ad0cd9f9e06003a", + "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", + "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", + "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", + "SRX11780889.psite.tsv.gz:md5,3650517af0545d8b522a4cadc7a9d380", + "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", + "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", + "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", + "SRX11780890.psite.tsv.gz:md5,163ab7bbceea7f1e55361552b295e56c", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1270,47 +1365,200 @@ "SRX11780890.para.py:md5,5f1696c5bf20116fa63363917e131284", "SRX11780890_qual.txt:md5,0f761538ecafb2718bd781c6e1fb7dc1", "SRX11780885.best_offset.txt:md5,1e6611858fd98bf4384cb121afb6707c", - "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", - "SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,87c80db54f46aac956f46a3ae09b23bc", - "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", - "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", - "SRX11780885.psite.tsv.gz:md5,517cfb43200a4d77598e7cea3d654460", "SRX11780885.psite_offset.tsv.gz:md5,8a9c12f2e2ed8ab033b0ef6094706e73", "SRX11780886.best_offset.txt:md5,787599a080c37b7d6eda470c13cc2563", - "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", - "SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,9b15a2401a9f0e42c060526f85596d8b", - "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", - "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", - "SRX11780886.psite.tsv.gz:md5,78de44e6dbda8f3914d52a068acde6bd", "SRX11780886.psite_offset.tsv.gz:md5,78798ac87401d666552fd6145abe58c7", "SRX11780887.best_offset.txt:md5,827cbf2c4231dd868dc6f93f8b6e83b0", - "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", - "SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,4fdbeb658fd750c97873f0a2d64ec3ef", - "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", - "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", - "SRX11780887.psite.tsv.gz:md5,7e510dc502bdf00f58c165237683cead", "SRX11780887.psite_offset.tsv.gz:md5,13629f9d786422375982dda7db270991", "SRX11780888.best_offset.txt:md5,df1bd7c66c950c943d200199d072f808", - "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", - "SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,26fb1fddeb9db9f4b46e027537af491b", - "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", - "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", - "SRX11780888.psite.tsv.gz:md5,f47672a5ec625ad56ad0cd9f9e06003a", "SRX11780888.psite_offset.tsv.gz:md5,6a8a86976ef7e185db81c2cb7e04014e", "SRX11780889.best_offset.txt:md5,d01cc2839b5415179f8f02b1fe583698", - "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", - "SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,62d1ad2c5d06dcc2f5e4b38037bac919", - "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", - "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", - "SRX11780889.psite.tsv.gz:md5,3650517af0545d8b522a4cadc7a9d380", "SRX11780889.psite_offset.tsv.gz:md5,b8f5920532f631997588149a2b4e1e48", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", - "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", - "SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,e51b52241818e27eb6f194af36dfc15a", - "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", - "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", - "SRX11780890.psite.tsv.gz:md5,163ab7bbceea7f1e55361552b295e56c", "SRX11780890.psite_offset.tsv.gz:md5,b42eac3c4b9e4c9b0af3be1aeb87907b", + "22.pdf:md5,ff96fe41668ac08c0f3f9fb5c0680f87", + "23.pdf:md5,08529012770c675ce13c0308055a1290", + "24.pdf:md5,b0a3898f7fadec66c3fd76b78a3418bb", + "25.pdf:md5,9df4036da6f993c6b0548a778bfb85b0", + "26.pdf:md5,acec96b469c275a24f922be767042597", + "27.pdf:md5,ad51ebb454a9aa4115a1b8fe6cb118fe", + "28.pdf:md5,3a17dcc005fb8aef99019df993854f3b", + "29.pdf:md5,f863b79366dddd2ad77938d47c70c7da", + "30.pdf:md5,1df1887c2dd3663e96b43861f7e59e33", + "31.pdf:md5,b761107c0da19e583028c543a2bb1dcb", + "32.pdf:md5,6c2010ef5a1bcd396f1039d503d0b839", + "33.pdf:md5,10f308fe63e34f991b400c56ae4c5f22", + "34.pdf:md5,d7d94b0e91b9f21ce301b4a0261f15b1", + "20.pdf:md5,b5fc90c57b7623d34058c1e1f443fb6d", + "21.pdf:md5,7a5a23bb048875f4b03337b8e6e95156", + "22.pdf:md5,f08621259571f7897d5c8fe8b9e70856", + "23.pdf:md5,5eaff57be21bba209e7e5af1a299f129", + "24.pdf:md5,258f5e25f4ad414af6121c64d37cee1b", + "25.pdf:md5,3a78ea64a531fd75c2d83561a828ed48", + "26.pdf:md5,7ee80192588b4e201d7fd5f8a66f41e7", + "27.pdf:md5,390fa464c605fd94f624c2d8d0d503ca", + "28.pdf:md5,42433b185f0a768b17d43b1b2ba931b5", + "29.pdf:md5,fcb5599915f9bb34f2ff62dab5cb14b6", + "30.pdf:md5,1fff444e652733a27461a81f2a67ecb7", + "31.pdf:md5,63c2402bdf282fa02a6880036916c868", + "32.pdf:md5,e7c3f1c201ace5a2a954625a28fd992c", + "33.pdf:md5,b9be9dc8a658af1aefc0674e6abf8216", + "20.pdf:md5,8615aa7e8fa2619c896f187af5050f60", + "21.pdf:md5,a1c0a0b5c2133153b73edc57b2c2624b", + "22.pdf:md5,9a196aa8fccded55354a50071b2d55f7", + "23.pdf:md5,b2dd6467fa97a9b0ba0eafbd6cb3ebb9", + "24.pdf:md5,b7c84bc0a67628130df0880d793606d9", + "25.pdf:md5,0ef497aa187a3ea3267767c3e43cfce2", + "26.pdf:md5,49857b5bf55625ec52f542da5874fbc0", + "27.pdf:md5,8a9130d836f3222512a0b5b2d82ad773", + "28.pdf:md5,5508f6569344f6005469fd6efb7cf7cd", + "29.pdf:md5,9e9674a9e06485a02f9d00e19732e795", + "30.pdf:md5,cf8831ebcc46d40261fd92a90541018b", + "31.pdf:md5,3cfc13f6c217c91f9f7d3df75881e37f", + "32.pdf:md5,dd41f7e9ff808717709a3ebbf19033a7", + "33.pdf:md5,b2098ef729aa410d3775a5ae07631471", + "34.pdf:md5,bcf62211aab1ac6d021c5a5ae522cc77", + "35.pdf:md5,8a6f2cee102059c9c86ef9270f2b5e64", + "36.pdf:md5,666bc0114b4b64997dff268fc708de00", + "37.pdf:md5,24f58ab956049e2baa6008bb16968b70", + "38.pdf:md5,e87ff5178637cc34ce79abe53a3b2af1", + "39.pdf:md5,5e6e9b8b4b6955c54d2d96c25345cf50", + "40.pdf:md5,88cb286404b09c11f7da3860bc042670", + "41.pdf:md5,e091b4424e44fada071ca7821716b682", + "21.pdf:md5,a6000f671bf6c78f62abb1999c834e7b", + "22.pdf:md5,e9f7d62ce8960269725f0394fde34059", + "23.pdf:md5,1af0e699d6c87cfc0af00f5a530e412e", + "24.pdf:md5,11cfd6cea431575856494ed011d6ee7b", + "25.pdf:md5,0fd3060f014a4c8eaec9f16f4bb4bb25", + "26.pdf:md5,5685f442d4f9645bb88ffc64da83cb0a", + "27.pdf:md5,0006c536f3db511a3975dc7499d63b56", + "28.pdf:md5,f09aca89061b38848325e0719ce1c13b", + "29.pdf:md5,45a96021976b700eb7eb4e856a7d12d0", + "30.pdf:md5,77bf2fd9ad91b659351dbc649ca754f7", + "22.pdf:md5,43d91f7522c80bcd923ae23eea0abe59", + "23.pdf:md5,316f9c23fd8188d3980a59d0d2b1fc0f", + "24.pdf:md5,95ddb0d075fdbccdbefb838aeffdc657", + "25.pdf:md5,35e629e635001cdb0375f79af914c1e9", + "26.pdf:md5,140a17db9ea2741843654733f5ffafb0", + "27.pdf:md5,b20894fe508714f5a12c72f21427fc7c", + "28.pdf:md5,0afa10bd2c3ff1b2b3fc0e6cf00935a2", + "29.pdf:md5,28b7883e599ed469e1e9ad5495421512", + "30.pdf:md5,dd8de48398e0db65659e5af83556fceb", + "31.pdf:md5,55149bf34914942d0460cf78cc9379e6", + "32.pdf:md5,337ae56ea06734f728ea8cd24dee60c3", + "21.pdf:md5,4a92f136adea850ec06ad15ef25a659e", + "22.pdf:md5,c71d558df12efe7575a574cbf98b9d71", + "23.pdf:md5,c1dc6a5a53ca5cc53a7c09afc4ff8a54", + "24.pdf:md5,bf83a6b59c0e12ac49d2ab571c476195", + "25.pdf:md5,e2fd74d3d3c33e437faecf35fe856776", + "26.pdf:md5,b0074a92d51cc3140c76fc1e58ce8c45", + "27.pdf:md5,d9442a3ff04b7f8bf526e15160942213", + "28.pdf:md5,a7b6e6d9db00712ea6a468d5644e146e", + "29.pdf:md5,8ae5eda9d5a0e15fb530971a39dbb93f", + "30.pdf:md5,2492123b60a19564bc2c470f9009e2f7", + "31.pdf:md5,1016080a85483299ec5d1c2279c7f512", + "32.pdf:md5,1aeadb318fa9a8a14fad2f44f4872799", + "33.pdf:md5,e5bc3e39838a190a668f0dcc6215f89d", + "SRX11780885.codon_usage.pdf:md5,6d9fe99ee3d61539c30e4c5ef086cc8e", + "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", + "SRX11780885.ends_heatmap.pdf:md5,33aed465e5e891df60c844699616a2e1", + "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", + "SRX11780885.frames.pdf:md5,4d4bf39daa1eae808993a108ea814111", + "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", + "SRX11780885.frames_stratified.pdf:md5,ace0790db1db84aae35f5af90564c6af", + "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", + "SRX11780885.length_bins_for_psite.pdf:md5,61cbd584d8d8f5dc2f7c69a4555fa635", + "SRX11780885.length_bins_for_psite.tsv:md5,acffe9ec8ae169747ff00edca341fbed", + "SRX11780885.length_distribution.pdf:md5,8b9d49a2a80e5bd28a8d455941c00ddd", + "SRX11780885.length_distribution.tsv:md5,3b9a5b39c0921175cc148f83f80cc021", + "SRX11780885.metaprofile_psite.pdf:md5,833e38e10c477455cb530f51451d49f9", + "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", + "SRX11780885.psite_region.pdf:md5,bc79d5abb1b0e0526809ef21e3856b4e", + "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", + "SRX11780886.codon_usage.pdf:md5,21b402e54fae6c7225ddfb38cbffb8ac", + "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", + "SRX11780886.ends_heatmap.pdf:md5,eaa9d8ed5dcdeae2b724a5c3e523df53", + "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", + "SRX11780886.frames.pdf:md5,8bdd7d8a4034cccef5c58235e500bb2a", + "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", + "SRX11780886.frames_stratified.pdf:md5,5c264e9f5ae4f50fb6b93c5fdf1ab1cc", + "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", + "SRX11780886.length_bins_for_psite.pdf:md5,a452e37e7f40bc3e525b7c1c70c4ae89", + "SRX11780886.length_bins_for_psite.tsv:md5,37bf7614ba447a9126ade1faed887c54", + "SRX11780886.length_distribution.pdf:md5,9c2b0758fcef7e5efa617578ca79a54f", + "SRX11780886.length_distribution.tsv:md5,189af46f3ef51420e9287bc4c5a7a3c7", + "SRX11780886.metaprofile_psite.pdf:md5,113d5f8b45c0f04c64c97d5b11801765", + "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", + "SRX11780886.psite_region.pdf:md5,b006d3fda32034c389f130c2eb9adbcd", + "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", + "SRX11780887.codon_usage.pdf:md5,778f1c064d09eda48cfc99dc1700255e", + "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", + "SRX11780887.ends_heatmap.pdf:md5,a9d7cca78f82f212953f115b37d7ae9e", + "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", + "SRX11780887.frames.pdf:md5,e901e50eafe3421fa1a50a917dcf86f9", + "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", + "SRX11780887.frames_stratified.pdf:md5,c4222461e5603ce69a64ca7457e0624a", + "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", + "SRX11780887.length_bins_for_psite.pdf:md5,9c8afbe0ea660c2423cef34af5615764", + "SRX11780887.length_bins_for_psite.tsv:md5,da69569999b3532e0a3b1eb6b3bfb8a4", + "SRX11780887.length_distribution.pdf:md5,c9f6e7361ea0975664a691052f4c104e", + "SRX11780887.length_distribution.tsv:md5,06e037385e45e601c59d9d2651811154", + "SRX11780887.metaprofile_psite.pdf:md5,5b4f8c2b0203b31debd6213806897d05", + "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", + "SRX11780887.psite_region.pdf:md5,638e649752db0764795476494e1f1f37", + "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", + "SRX11780888.codon_usage.pdf:md5,55b12e349d7bac3a0c66b3ceacbb0c3f", + "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", + "SRX11780888.ends_heatmap.pdf:md5,abe6bdc3b0ec1c9b6889191a04497a4b", + "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", + "SRX11780888.frames.pdf:md5,6998d4e4eb1306ffe72b2b47e9b6e68a", + "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", + "SRX11780888.frames_stratified.pdf:md5,065989ee280df06eded6dadf1fadfacd", + "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", + "SRX11780888.length_bins_for_psite.pdf:md5,2399009214a300f809cfe370316d7935", + "SRX11780888.length_bins_for_psite.tsv:md5,55e239b32b68a229155a572a95594dae", + "SRX11780888.length_distribution.pdf:md5,3993e8b29301363111991a2d3b2c0070", + "SRX11780888.length_distribution.tsv:md5,240fbe4c42322625f840478a38f239a7", + "SRX11780888.metaprofile_psite.pdf:md5,12d855ef6f94939eac918ed050e5ba54", + "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", + "SRX11780888.psite_region.pdf:md5,64cb644ac90d6f1cf5aa31d96329ede6", + "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", + "SRX11780889.codon_usage.pdf:md5,f1365ffa9f2f68cc9362345c57b5f361", + "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", + "SRX11780889.ends_heatmap.pdf:md5,25dc463bf4b35cdcbcc9e8e684e82233", + "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", + "SRX11780889.frames.pdf:md5,2b8f1e3bc3d791ff1168b30dc3c42923", + "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", + "SRX11780889.frames_stratified.pdf:md5,9e0c6978812500ad12fe2e45c5d70a0f", + "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", + "SRX11780889.length_bins_for_psite.pdf:md5,b2f282a6f615a477283b036e006e535f", + "SRX11780889.length_bins_for_psite.tsv:md5,2a3f0c15f19e5ec9031e0f8b13dc7d0d", + "SRX11780889.length_distribution.pdf:md5,923e699815bb2182b2f5cb6858073962", + "SRX11780889.length_distribution.tsv:md5,afd2a7c32de7e20247c36c6068e1f4c5", + "SRX11780889.metaprofile_psite.pdf:md5,c3607af7eb62d3f7e1e5e0b0e22dd2b4", + "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", + "SRX11780889.psite_region.pdf:md5,e7588edba46cf8fc0db46ce8ddc643b2", + "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", + "SRX11780890.codon_usage.pdf:md5,4bb9478751efcd024d4e5a01c9b0e93b", + "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", + "SRX11780890.ends_heatmap.pdf:md5,ee16bbbe9e0bd5c022fca0916655d23b", + "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", + "SRX11780890.frames.pdf:md5,be28fe9ce8055223303e71015dd3005e", + "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", + "SRX11780890.frames_stratified.pdf:md5,dcbfa207fb28353f8e58dd07e6b25de9", + "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", + "SRX11780890.length_bins_for_psite.pdf:md5,2794ef8b1645fded7787591f5b5982b2", + "SRX11780890.length_bins_for_psite.tsv:md5,d847ef721250472267b53a80d4e3951e", + "SRX11780890.length_distribution.pdf:md5,9d852a903c936efdde8f069143fc8221", + "SRX11780890.length_distribution.tsv:md5,0e59ff544796c53e220547b820b0137d", + "SRX11780890.metaprofile_psite.pdf:md5,7a401300597ec7f8f5f212a8b429e14c", + "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", + "SRX11780890.psite_region.pdf:md5,08fbefbf1eba2985ea40eaf060d8b5f8", + "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", + "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", + "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8", + "ribowaltz_metaprofile_stop_mqc.json:md5,9d47939e48ad3a6f47a83dfc3f4cba5d", + "ribowaltz_psite_regions_mqc.tsv:md5,31c7d9a993d3203518ab2a1f66710d55", "treated_vs_control.R_sessionInfo.log:md5,3623a50b4668bfebf502bf7080800996" ] ], @@ -1318,6 +1566,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-12T18:09:37.017438328" + "timestamp": "2026-01-05T13:06:53.847627617" } } \ No newline at end of file diff --git a/tests/deltate.nf.test.snap b/tests/deltate.nf.test.snap index 6fbd7941..16198da0 100644 --- a/tests/deltate.nf.test.snap +++ b/tests/deltate.nf.test.snap @@ -323,40 +323,47 @@ "multiqc/star", "multiqc/star/multiqc_report.html", "multiqc/star/multiqc_report_data", + "multiqc/star/multiqc_report_data/bowtie2_pe_plot.txt", + "multiqc/star/multiqc_report_data/bowtie2_se_plot.txt", "multiqc/star/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star/multiqc_report_data/fastqc-1-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc-1_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_duplication_levels_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_top_overrepresented_sequences_table.txt", - "multiqc/star/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/llms-full.txt", "multiqc/star/multiqc_report_data/multiqc.log", "multiqc/star/multiqc_report_data/multiqc.parquet", + "multiqc/star/multiqc_report_data/multiqc_bowtie2_bowtie2_rrna.txt", "multiqc/star/multiqc_report_data/multiqc_citations.txt", "multiqc/star/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star/multiqc_report_data/multiqc_data.json", - "multiqc/star/multiqc_report_data/multiqc_fastqc.txt", - "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc-1.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", "multiqc/star/multiqc_report_data/multiqc_general_stats.txt", "multiqc/star/multiqc_report_data/multiqc_ribotish.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_1_psite_regions_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_2_frames_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_3_metaprofile_start_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_4_metaprofile_stop_plot.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_stats.txt", @@ -376,35 +383,43 @@ "multiqc/star/multiqc_report_data/star_summary_table.txt", "multiqc/star/multiqc_report_plots", "multiqc/star/multiqc_report_plots/pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_pe_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_pe_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_se_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_se_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_duplication_levels_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_top_overrepresented_sequences_table.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_frame_proportions.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_read_length_line.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_1_psite_regions_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_2_frames_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_3_metaprofile_start_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_4_metaprofile_stop_plot.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -420,35 +435,43 @@ "multiqc/star/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star/multiqc_report_plots/png", + "multiqc/star/multiqc_report_plots/png/bowtie2_pe_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_pe_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_se_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_se_plot-pct.png", "multiqc/star/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_duplication_levels_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_top_overrepresented_sequences_table.png", - "multiqc/star/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/ribotish_frame_proportions.png", "multiqc/star/multiqc_report_plots/png/ribotish_read_length_line.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_1_psite_regions_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_2_frames_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_3_metaprofile_start_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_4_metaprofile_stop_plot.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-pct-table.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-table.png", "multiqc/star/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -464,35 +487,43 @@ "multiqc/star/multiqc_report_plots/png/star_alignment_plot-pct.png", "multiqc/star/multiqc_report_plots/png/star_summary_table.png", "multiqc/star/multiqc_report_plots/svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_pe_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_pe_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_se_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_se_plot-pct.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_duplication_levels_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_top_overrepresented_sequences_table.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_frame_proportions.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_read_length_line.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_1_psite_regions_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_2_frames_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_3_metaprofile_start_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_4_metaprofile_stop_plot.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -531,6 +562,32 @@ "orf_predictions/ribotish_all/allsamples_all.txt", "orf_predictions/ribotish_all/allsamples_pred.txt", "orf_predictions/ribotish_all/allsamples_transprofile.py", + "other", + "other/ribowaltz", + "other/ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780885.psite.tsv.gz", + "other/ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780886.psite.tsv.gz", + "other/ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780887.psite.tsv.gz", + "other/ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780888.psite.tsv.gz", + "other/ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780889.psite.tsv.gz", + "other/ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780890.psite.tsv.gz", "pipeline_info", "pipeline_info/nf_core_riboseq_software_mqc_versions.yml", "preprocessing", @@ -893,188 +950,211 @@ "riboseq_qc/ribotish/SRX11780890.para.py", "riboseq_qc/ribotish/SRX11780890_qual.pdf", "riboseq_qc/ribotish/SRX11780890_qual.txt", + "riboseq_qc/ribowaltz", + "riboseq_qc/ribowaltz/SRX11780885.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780885.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780886.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780886.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780887.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780887.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780888.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780888.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780889.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780889.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780890.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780890.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/offset_plot", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/35.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/36.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/37.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/38.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/39.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/40.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/41.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/33.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.tsv", "ribowaltz", - "ribowaltz/SRX11780885.best_offset.txt", - "ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780885.psite.tsv.gz", - "ribowaltz/SRX11780885.psite_offset.tsv.gz", - "ribowaltz/SRX11780886.best_offset.txt", - "ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780886.psite.tsv.gz", - "ribowaltz/SRX11780886.psite_offset.tsv.gz", - "ribowaltz/SRX11780887.best_offset.txt", - "ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780887.psite.tsv.gz", - "ribowaltz/SRX11780887.psite_offset.tsv.gz", - "ribowaltz/SRX11780888.best_offset.txt", - "ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780888.psite.tsv.gz", - "ribowaltz/SRX11780888.psite_offset.tsv.gz", - "ribowaltz/SRX11780889.best_offset.txt", - "ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780889.psite.tsv.gz", - "ribowaltz/SRX11780889.psite_offset.tsv.gz", - "ribowaltz/SRX11780890.best_offset.txt", - "ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780890.psite.tsv.gz", - "ribowaltz/SRX11780890.psite_offset.tsv.gz", - "ribowaltz/offset_plot", - "ribowaltz/offset_plot/SRX11780885", - "ribowaltz/offset_plot/SRX11780885/22.pdf", - "ribowaltz/offset_plot/SRX11780885/23.pdf", - "ribowaltz/offset_plot/SRX11780885/24.pdf", - "ribowaltz/offset_plot/SRX11780885/25.pdf", - "ribowaltz/offset_plot/SRX11780885/26.pdf", - "ribowaltz/offset_plot/SRX11780885/27.pdf", - "ribowaltz/offset_plot/SRX11780885/28.pdf", - "ribowaltz/offset_plot/SRX11780885/29.pdf", - "ribowaltz/offset_plot/SRX11780885/30.pdf", - "ribowaltz/offset_plot/SRX11780885/31.pdf", - "ribowaltz/offset_plot/SRX11780885/32.pdf", - "ribowaltz/offset_plot/SRX11780885/33.pdf", - "ribowaltz/offset_plot/SRX11780885/34.pdf", - "ribowaltz/offset_plot/SRX11780886", - "ribowaltz/offset_plot/SRX11780886/20.pdf", - "ribowaltz/offset_plot/SRX11780886/21.pdf", - "ribowaltz/offset_plot/SRX11780886/22.pdf", - "ribowaltz/offset_plot/SRX11780886/23.pdf", - "ribowaltz/offset_plot/SRX11780886/24.pdf", - "ribowaltz/offset_plot/SRX11780886/25.pdf", - "ribowaltz/offset_plot/SRX11780886/26.pdf", - "ribowaltz/offset_plot/SRX11780886/27.pdf", - "ribowaltz/offset_plot/SRX11780886/28.pdf", - "ribowaltz/offset_plot/SRX11780886/29.pdf", - "ribowaltz/offset_plot/SRX11780886/30.pdf", - "ribowaltz/offset_plot/SRX11780886/31.pdf", - "ribowaltz/offset_plot/SRX11780886/32.pdf", - "ribowaltz/offset_plot/SRX11780886/33.pdf", - "ribowaltz/offset_plot/SRX11780887", - "ribowaltz/offset_plot/SRX11780887/20.pdf", - "ribowaltz/offset_plot/SRX11780887/21.pdf", - "ribowaltz/offset_plot/SRX11780887/22.pdf", - "ribowaltz/offset_plot/SRX11780887/23.pdf", - "ribowaltz/offset_plot/SRX11780887/24.pdf", - "ribowaltz/offset_plot/SRX11780887/25.pdf", - "ribowaltz/offset_plot/SRX11780887/26.pdf", - "ribowaltz/offset_plot/SRX11780887/27.pdf", - "ribowaltz/offset_plot/SRX11780887/28.pdf", - "ribowaltz/offset_plot/SRX11780887/29.pdf", - "ribowaltz/offset_plot/SRX11780887/30.pdf", - "ribowaltz/offset_plot/SRX11780887/31.pdf", - "ribowaltz/offset_plot/SRX11780887/32.pdf", - "ribowaltz/offset_plot/SRX11780887/33.pdf", - "ribowaltz/offset_plot/SRX11780887/34.pdf", - "ribowaltz/offset_plot/SRX11780887/35.pdf", - "ribowaltz/offset_plot/SRX11780887/36.pdf", - "ribowaltz/offset_plot/SRX11780887/37.pdf", - "ribowaltz/offset_plot/SRX11780887/38.pdf", - "ribowaltz/offset_plot/SRX11780887/39.pdf", - "ribowaltz/offset_plot/SRX11780887/40.pdf", - "ribowaltz/offset_plot/SRX11780887/41.pdf", - "ribowaltz/offset_plot/SRX11780888", - "ribowaltz/offset_plot/SRX11780888/21.pdf", - "ribowaltz/offset_plot/SRX11780888/22.pdf", - "ribowaltz/offset_plot/SRX11780888/23.pdf", - "ribowaltz/offset_plot/SRX11780888/24.pdf", - "ribowaltz/offset_plot/SRX11780888/25.pdf", - "ribowaltz/offset_plot/SRX11780888/26.pdf", - "ribowaltz/offset_plot/SRX11780888/27.pdf", - "ribowaltz/offset_plot/SRX11780888/28.pdf", - "ribowaltz/offset_plot/SRX11780888/29.pdf", - "ribowaltz/offset_plot/SRX11780888/30.pdf", - "ribowaltz/offset_plot/SRX11780889", - "ribowaltz/offset_plot/SRX11780889/22.pdf", - "ribowaltz/offset_plot/SRX11780889/23.pdf", - "ribowaltz/offset_plot/SRX11780889/24.pdf", - "ribowaltz/offset_plot/SRX11780889/25.pdf", - "ribowaltz/offset_plot/SRX11780889/26.pdf", - "ribowaltz/offset_plot/SRX11780889/27.pdf", - "ribowaltz/offset_plot/SRX11780889/28.pdf", - "ribowaltz/offset_plot/SRX11780889/29.pdf", - "ribowaltz/offset_plot/SRX11780889/30.pdf", - "ribowaltz/offset_plot/SRX11780889/31.pdf", - "ribowaltz/offset_plot/SRX11780889/32.pdf", - "ribowaltz/offset_plot/SRX11780890", - "ribowaltz/offset_plot/SRX11780890/21.pdf", - "ribowaltz/offset_plot/SRX11780890/22.pdf", - "ribowaltz/offset_plot/SRX11780890/23.pdf", - "ribowaltz/offset_plot/SRX11780890/24.pdf", - "ribowaltz/offset_plot/SRX11780890/25.pdf", - "ribowaltz/offset_plot/SRX11780890/26.pdf", - "ribowaltz/offset_plot/SRX11780890/27.pdf", - "ribowaltz/offset_plot/SRX11780890/28.pdf", - "ribowaltz/offset_plot/SRX11780890/29.pdf", - "ribowaltz/offset_plot/SRX11780890/30.pdf", - "ribowaltz/offset_plot/SRX11780890/31.pdf", - "ribowaltz/offset_plot/SRX11780890/32.pdf", - "ribowaltz/offset_plot/SRX11780890/33.pdf", - "ribowaltz/ribowaltz_qc", - "ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "ribowaltz/ribowaltz_frames_mqc.tsv", + "ribowaltz/ribowaltz_metaprofile_start_mqc.json", + "ribowaltz/ribowaltz_metaprofile_stop_mqc.json", + "ribowaltz/ribowaltz_psite_regions_mqc.tsv", "translational_efficiency", "translational_efficiency/deltate", "translational_efficiency/deltate/treated_vs_control.DESeqDataSet.rds", @@ -1158,33 +1238,42 @@ "SRX11780890.genome.sorted.bam.idxstats:md5,3a0b29a35c233c8a44da429c0c1c4051", "SRX11780890.transcriptome.sorted.bam.flagstat:md5,87173978a2990cd5da861ad20b0b6982", "SRX11780890.transcriptome.sorted.bam.idxstats:md5,ae7f1daff6764bbc167742d19c99d587", + "bowtie2_pe_plot.txt:md5,b4dc3c205f64fed5094f56622512451b", + "bowtie2_se_plot.txt:md5,1a9cb4b686308088e524ef2b313e2f49", "cutadapt_filtered_reads_plot.txt:md5,ff95c965185e62ff5914a5c60e7a268f", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,319e9bb90c170c4b0207d644926bf69a", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,6ed5bbd0961572352d1614cc1f25f29d", - "fastqc-1-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc-1_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", - "fastqc-1_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", - "fastqc-1_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", - "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", - "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", - "fastqc-1_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", - "fastqc-1_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", - "fastqc-1_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", - "fastqc-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", - "fastqc_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", - "fastqc_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", - "fastqc_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", - "fastqc_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", - "fastqc_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", + "fastqc_raw_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", + "fastqc_raw_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,cdd555433a5c5bae529cd086512cbb69", "fastqc_sequence_length_distribution_plot.txt:md5,d3f33f3eda7927b061fc3cdec99e8f4e", - "multiqc_citations.txt:md5,639700223364dc6a161895ecdb029710", + "fastqc_trimmed-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", + "fastqc_trimmed_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", + "fastqc_trimmed_top_overrepresented_sequences_table.txt:md5,18dd505c347a3faac767f31b740265d4", + "multiqc_bowtie2_bowtie2_rrna.txt:md5,3370acc7d4ccbfb2c7535f2c962449ed", + "multiqc_citations.txt:md5,e2b5d6b0dcf0f2e6cd2771fa8cb7039a", "multiqc_cutadapt.txt:md5,e6031ab468a23c95b6989a6ce9e081f5", - "multiqc_fastqc.txt:md5,435f987c78b50ab1dfe18640246f580b", - "multiqc_fastqc_fastqc-1.txt:md5,c8ce8940114de9321e6de124b6cb4c18", + "multiqc_fastqc_fastqc_raw.txt:md5,435f987c78b50ab1dfe18640246f580b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,c8ce8940114de9321e6de124b6cb4c18", "multiqc_ribotish.txt:md5,21546543970095b3bcc6ab20ac0425e7", + "multiqc_ribowaltz_1_psite_regions_plot.txt:md5,0a054c20541cee8a35a98e841d828837", + "multiqc_ribowaltz_2_frames_plot.txt:md5,2d3805092494ba14f3cba0d862c34656", + "multiqc_ribowaltz_3_metaprofile_start_plot.txt:md5,4d63cc9e6fbcdac63cb222eb1c2709a9", + "multiqc_ribowaltz_4_metaprofile_stop_plot.txt:md5,dedfc06570e87423138ddf8ca9bdc23e", "multiqc_samtools_flagstat.txt:md5,9fc0f9e799ae50c4b353b70aa1748b43", "multiqc_samtools_idxstats.txt:md5,acc2f751f8006c65cac9f52e5d408a2b", "multiqc_samtools_stats.txt:md5,086c61cbb732ee1ea68bbd10760dd33f", @@ -1221,6 +1310,30 @@ "allsamples_all.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_pred.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_transprofile.py:md5,51abc67be45f2a68677a551c887ff930", + "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", + "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", + "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", + "SRX11780885.psite.tsv.gz:md5,8276459cd5f05ae92510e9c983f643db", + "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", + "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", + "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", + "SRX11780886.psite.tsv.gz:md5,d5776b81cdd2af8504fc3db2041da515", + "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", + "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", + "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", + "SRX11780887.psite.tsv.gz:md5,bec9bc165cd21e17fc03a86cb87005c5", + "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", + "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", + "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", + "SRX11780888.psite.tsv.gz:md5,1e91a44a68e1918506962648d56a9192", + "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", + "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", + "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", + "SRX11780889.psite.tsv.gz:md5,df4d090347750c96c3b331dab0f582a9", + "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", + "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", + "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", + "SRX11780890.psite.tsv.gz:md5,ad3e7a4abdba33a47bfe369cd7f2a725", "SRX11780879.bowtie2.log:md5,44dd58926df16decd27314e7c42ba3b9", "SRX11780880.bowtie2.log:md5,69100acbfbda03335ba3ac7cbffdb16f", "SRX11780881.bowtie2.log:md5,99b022d64a54c14bacb95d633554e613", @@ -1296,47 +1409,200 @@ "SRX11780890.para.py:md5,5f1696c5bf20116fa63363917e131284", "SRX11780890_qual.txt:md5,0f761538ecafb2718bd781c6e1fb7dc1", "SRX11780885.best_offset.txt:md5,1e6611858fd98bf4384cb121afb6707c", - "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", - "SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,87c80db54f46aac956f46a3ae09b23bc", - "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", - "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", - "SRX11780885.psite.tsv.gz:md5,8276459cd5f05ae92510e9c983f643db", "SRX11780885.psite_offset.tsv.gz:md5,2ef8627be1603928b16f5fb561ac47b6", "SRX11780886.best_offset.txt:md5,787599a080c37b7d6eda470c13cc2563", - "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", - "SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,9b15a2401a9f0e42c060526f85596d8b", - "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", - "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", - "SRX11780886.psite.tsv.gz:md5,d5776b81cdd2af8504fc3db2041da515", "SRX11780886.psite_offset.tsv.gz:md5,583bea05a8cacd96adec469132c968f5", "SRX11780887.best_offset.txt:md5,827cbf2c4231dd868dc6f93f8b6e83b0", - "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", - "SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,4fdbeb658fd750c97873f0a2d64ec3ef", - "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", - "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", - "SRX11780887.psite.tsv.gz:md5,bec9bc165cd21e17fc03a86cb87005c5", "SRX11780887.psite_offset.tsv.gz:md5,14eebe2a609db07671c22ba4486e8d99", "SRX11780888.best_offset.txt:md5,df1bd7c66c950c943d200199d072f808", - "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", - "SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,26fb1fddeb9db9f4b46e027537af491b", - "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", - "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", - "SRX11780888.psite.tsv.gz:md5,1e91a44a68e1918506962648d56a9192", "SRX11780888.psite_offset.tsv.gz:md5,b52ce5b4cd9a95231d02fc5fed83af70", "SRX11780889.best_offset.txt:md5,d01cc2839b5415179f8f02b1fe583698", - "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", - "SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,62d1ad2c5d06dcc2f5e4b38037bac919", - "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", - "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", - "SRX11780889.psite.tsv.gz:md5,df4d090347750c96c3b331dab0f582a9", "SRX11780889.psite_offset.tsv.gz:md5,e73bb4cd13df6f92efdbaa7dcf380784", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", - "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", - "SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,e51b52241818e27eb6f194af36dfc15a", - "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", - "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", - "SRX11780890.psite.tsv.gz:md5,ad3e7a4abdba33a47bfe369cd7f2a725", "SRX11780890.psite_offset.tsv.gz:md5,4c640cbe8c24465fa1758951af308534", + "22.pdf:md5,e420fbd17e410e63ecb6bc5c148a9027", + "23.pdf:md5,0da0b81ace774fb3adb50ac92bfa2837", + "24.pdf:md5,18db6f0b6b582bdaf3882746c0fb193b", + "25.pdf:md5,59783ebe7c3e6fa7b9932e9e88f81747", + "26.pdf:md5,36c07a6da60cf88393f27b798df24997", + "27.pdf:md5,3ff784471dd7be92bb5f6e3c6220aeac", + "28.pdf:md5,ee8a0f06e132965966c5cddbd331fee7", + "29.pdf:md5,ea3bfe25a85bda489d5c1a094322d16c", + "30.pdf:md5,8aabc0de46f2d6758c1eea728179f24e", + "31.pdf:md5,016ed138663b2cca30b1624269675b5e", + "32.pdf:md5,5ed2b6f441ed625d03189138ecdb6650", + "33.pdf:md5,e51a503da259824f1c9b6ea9a20d7121", + "34.pdf:md5,a3dbc2912f763cf4410597c32e80b2b9", + "20.pdf:md5,1b94766fb1136e56b737323055e05510", + "21.pdf:md5,2401f54c4929caa3ac8b0928ff800622", + "22.pdf:md5,c6f462d7fac004954aeaa3b72a6edb95", + "23.pdf:md5,198e4cbba0ab5f0cb6e1679b3e1090cb", + "24.pdf:md5,6a6f386feb9e40ad15aa3145e72b381c", + "25.pdf:md5,6f7d7264bded8343bd44677ac28d2b09", + "26.pdf:md5,38e0fe4d901ea91f6d69ea26ba47c3bb", + "27.pdf:md5,31f28c21638a2ec5859ac93312402948", + "28.pdf:md5,fbc490183b5c2efb2f7209e12d4e0330", + "29.pdf:md5,7281cba67177732ed09fdae312ce3085", + "30.pdf:md5,bf7b11f43129fa3bfbc7c7c68b09a8c1", + "31.pdf:md5,9229acd16d7bdd2402cfe17d98e3c606", + "32.pdf:md5,c512d5f4b311136247feddf166e65bdb", + "33.pdf:md5,1fc2dd5d779f5840be5df16fea307f34", + "20.pdf:md5,7bc8dfd508164d57ab4ea1876416a9e5", + "21.pdf:md5,ccf2192dc981377cf6a4e0cba3925769", + "22.pdf:md5,0437c16e8f491c6082800fc561d0c151", + "23.pdf:md5,e21271d8e1c7a8c7da166bad315645dd", + "24.pdf:md5,12f8089d806fdef77b693abb6bdd53ce", + "25.pdf:md5,64bcad4c8a44533b452e11c4fc3da704", + "26.pdf:md5,317f8e60fcfdf280e90ed5ef5cdb7fc7", + "27.pdf:md5,1dcf71705a57fcb1774dc75efe40fcd0", + "28.pdf:md5,d12ae70dca790222e39e35ee599f63f9", + "29.pdf:md5,5c8551b35a3906206f187462ba27f35d", + "30.pdf:md5,a265c55756944a99e43fe8bc68c19293", + "31.pdf:md5,2359e72378ec8f5a87302e8fff2d3074", + "32.pdf:md5,7a44b8b00e18b7b8a4c35cf4fb07152d", + "33.pdf:md5,eae4ce4c666359a49c4d9d2f9f049061", + "34.pdf:md5,ab8cce1289e482c2e0b31d50698ed402", + "35.pdf:md5,55d0ec6d620a1d19a1f0fdab0b0cbdb9", + "36.pdf:md5,ddc49d924c3751903cfcb654cf9be1a7", + "37.pdf:md5,d45d8015bcc3d6e4149990b30e480ca2", + "38.pdf:md5,aba3447dd5543363128bf848cca246cf", + "39.pdf:md5,e883a6776bf6a098bc92f1088bc856a3", + "40.pdf:md5,616da789b1c98bbbee6cbcfd86fa551f", + "41.pdf:md5,fdaf259171e0cbc79cd1e16a0dad7e01", + "21.pdf:md5,9b37b12431ec0509889bf2f2a7bdf13c", + "22.pdf:md5,20def5827ecb8f40bba38445d11405bd", + "23.pdf:md5,4f0d4e61730f81f4d6f2ec8fa625d34a", + "24.pdf:md5,7067ff38357082ca26328ee762217635", + "25.pdf:md5,3c7958e8449fc32537d7c3e9e08902a1", + "26.pdf:md5,0b657d71f8a6eb4f0ccf7e88e146008b", + "27.pdf:md5,784c2f458524e8baf2013629326201ae", + "28.pdf:md5,735f72320833b3c1520383baa36053e5", + "29.pdf:md5,71cc5ce4d4408a7a64ab0b819b9661e8", + "30.pdf:md5,020609799b92f9ab766fa6e0a56c1f18", + "22.pdf:md5,f022362fb4dd6a7296cb58056f731b9e", + "23.pdf:md5,916a64de6cc7f523e9e5c0471514055b", + "24.pdf:md5,4aed0321122c9156e436be9a839d2cbd", + "25.pdf:md5,346893619e7b9c0f41acf379aa4c30d3", + "26.pdf:md5,596976611c2b2528add434f643d6ff92", + "27.pdf:md5,5029271934f43e09935f907041de9f8c", + "28.pdf:md5,67fa9cb654d3cb799dc0a3fc98c946b6", + "29.pdf:md5,0df9fb630eebba04dba6328b3ac4f721", + "30.pdf:md5,396d4894a68407a2e61300f9571d37e7", + "31.pdf:md5,d61ee795a30c61f4836d1c318d7b2fbc", + "32.pdf:md5,81662cbf46872ade3711c77ee77b3015", + "21.pdf:md5,fa0ddbff587cfe6734042d4d5acf3620", + "22.pdf:md5,e3322450d3bfbeea1ce3ff5a85243002", + "23.pdf:md5,7f11a7f38bcc98f3838db11a08e23da2", + "24.pdf:md5,c78a1c7455d7b75543349f89b3304b88", + "25.pdf:md5,04aa15f67617b72447240e5123dd634a", + "26.pdf:md5,160bfc510ec70d75b99c357bf778511d", + "27.pdf:md5,06bf380db0046317bb676130338caa0b", + "28.pdf:md5,0b3b50556988c04bdfc086ba4d50cd7f", + "29.pdf:md5,151d2e19b2a31f12257b518b8a8cc3aa", + "30.pdf:md5,6196b9e83299987f5fdd10933457c679", + "31.pdf:md5,2c08a11a51215c01761e0b8e7d4f7173", + "32.pdf:md5,84f0adcb985789280a4b67f150aa876b", + "33.pdf:md5,586ddcaea1558644f0540d4d2efc54f2", + "SRX11780885.codon_usage.pdf:md5,3979d8931a1c22435578e3f68e4b2088", + "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", + "SRX11780885.ends_heatmap.pdf:md5,77ac2c50eea98b5ab7b46d1db8dc5a59", + "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", + "SRX11780885.frames.pdf:md5,caefae112aea637068cb55fc6999818f", + "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", + "SRX11780885.frames_stratified.pdf:md5,83ecb72b9a035398a0320a487c04702b", + "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", + "SRX11780885.length_bins_for_psite.pdf:md5,6bb5606c56040540760118ae9e35bf3d", + "SRX11780885.length_bins_for_psite.tsv:md5,b6fd5abd7f639276df10698b94d3cc52", + "SRX11780885.length_distribution.pdf:md5,62e40029d295f52f6d5bf4009dfc45e7", + "SRX11780885.length_distribution.tsv:md5,82bee1b71c13feb716f000d4982ed3cf", + "SRX11780885.metaprofile_psite.pdf:md5,df461936abff78aec01a388e72f0d274", + "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", + "SRX11780885.psite_region.pdf:md5,b676c7d00cf27bec89acaf51281b78ec", + "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", + "SRX11780886.codon_usage.pdf:md5,dac0a10dd31a820e59ebd64ee3846df3", + "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", + "SRX11780886.ends_heatmap.pdf:md5,eb9079567496a060d8bb68ed675a9bd9", + "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", + "SRX11780886.frames.pdf:md5,b36f2eeac22f5897d0872294eb8480d9", + "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", + "SRX11780886.frames_stratified.pdf:md5,d44a0c9ee59644a4d4557a255e765445", + "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", + "SRX11780886.length_bins_for_psite.pdf:md5,65bca0a0e7857bf70378f73c4f3a5c7a", + "SRX11780886.length_bins_for_psite.tsv:md5,e226199778c919ad4da4d6ff39379742", + "SRX11780886.length_distribution.pdf:md5,c0a65db004ed8f4d20bc457c2e69cf65", + "SRX11780886.length_distribution.tsv:md5,b272c92a918a405b2cccba30ff0405e1", + "SRX11780886.metaprofile_psite.pdf:md5,f4b3b7fefa1da8b21367645c9567e02b", + "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", + "SRX11780886.psite_region.pdf:md5,98a7ec60951edfde99cb551047dd02b5", + "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", + "SRX11780887.codon_usage.pdf:md5,896e9179925e55602391d52a93e7b2c4", + "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", + "SRX11780887.ends_heatmap.pdf:md5,748edcee82c95e6a499765172331feae", + "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", + "SRX11780887.frames.pdf:md5,9dcb834a3ab2cac6889876271c37bf4e", + "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", + "SRX11780887.frames_stratified.pdf:md5,6621056d6fc3cc56f3ac0c99ecdaeff6", + "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", + "SRX11780887.length_bins_for_psite.pdf:md5,20a09c2daa39f5297cf37ac7cc368579", + "SRX11780887.length_bins_for_psite.tsv:md5,545a6874f9f3d82c26f28b04977dfcb8", + "SRX11780887.length_distribution.pdf:md5,d73d72d403245d8c455b2286f1b0b432", + "SRX11780887.length_distribution.tsv:md5,ce512154c88e9cee2c2a9509f82918e8", + "SRX11780887.metaprofile_psite.pdf:md5,7710bdc773ced5c0c9d040ed2eae4ee5", + "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", + "SRX11780887.psite_region.pdf:md5,232fd20365978dde59655f79ee437822", + "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", + "SRX11780888.codon_usage.pdf:md5,4d5cd6fecba80b8643a9a7011e125f79", + "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", + "SRX11780888.ends_heatmap.pdf:md5,67138d42d9eaa0b4992298d915a09d94", + "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", + "SRX11780888.frames.pdf:md5,19fb4b2cbe0796cc4775a23dd333ea94", + "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", + "SRX11780888.frames_stratified.pdf:md5,24e137a5eec062403cab9edbb7634a45", + "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", + "SRX11780888.length_bins_for_psite.pdf:md5,bb93faae2665886a4ac73378173160da", + "SRX11780888.length_bins_for_psite.tsv:md5,f7d9223b388a77dd91c5a41aa89134c7", + "SRX11780888.length_distribution.pdf:md5,b0e4a1b1bf220eb58f389e35d929de48", + "SRX11780888.length_distribution.tsv:md5,3e5ef7ee2e090123cf4c2bc6ea71bb01", + "SRX11780888.metaprofile_psite.pdf:md5,1ce598b1092b7c4a03a3c17a6b89d2ec", + "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", + "SRX11780888.psite_region.pdf:md5,b88af13a96a53e5a665a40f222b4324d", + "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", + "SRX11780889.codon_usage.pdf:md5,dc60791aa4c9b41ee5fd8bdc3ea4f61f", + "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", + "SRX11780889.ends_heatmap.pdf:md5,bdd92550f4b969e70d83f574b6a030de", + "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", + "SRX11780889.frames.pdf:md5,eb724ed8ff0b9de5f0a62fd23e437062", + "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", + "SRX11780889.frames_stratified.pdf:md5,422d1340ef5347d4fa35b3e81d23e0ca", + "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", + "SRX11780889.length_bins_for_psite.pdf:md5,ead7f676e0b94c00f45567f012c433f4", + "SRX11780889.length_bins_for_psite.tsv:md5,488b91e071d8bcd3d8933974bd6cf952", + "SRX11780889.length_distribution.pdf:md5,7ee7e138b403f9dc6d1461a7b5b4fd5e", + "SRX11780889.length_distribution.tsv:md5,cc5ae4ad914c8afba7726dccc47f9cd0", + "SRX11780889.metaprofile_psite.pdf:md5,3037cd0c68fe42abf633574e22abdd0a", + "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", + "SRX11780889.psite_region.pdf:md5,3d245cde8530c5bd8115d97ab6405455", + "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", + "SRX11780890.codon_usage.pdf:md5,bb41f0f85f8decf88b98478b4b386983", + "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", + "SRX11780890.ends_heatmap.pdf:md5,976114a83fbc33a75e79d78d06656409", + "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", + "SRX11780890.frames.pdf:md5,fefb085c84f11618c3e5bea93dbf5855", + "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", + "SRX11780890.frames_stratified.pdf:md5,131aa3cbf3ec730d509e8c6b8dd7bff4", + "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", + "SRX11780890.length_bins_for_psite.pdf:md5,4b12ae3083276fcbafb0613f46d3c4e8", + "SRX11780890.length_bins_for_psite.tsv:md5,5bed6cd6fb8f944a6e0e7d9325dce6c3", + "SRX11780890.length_distribution.pdf:md5,60625ddce69b081a54e00d16a0dbf02a", + "SRX11780890.length_distribution.tsv:md5,2ee60618861bde90a7ebcbba7013adfe", + "SRX11780890.metaprofile_psite.pdf:md5,1a1c6d9530a91214267a545024f7d3ca", + "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", + "SRX11780890.psite_region.pdf:md5,24a561b95394cbcaa23b3fa42e9d031e", + "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", + "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", + "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8", + "ribowaltz_metaprofile_stop_mqc.json:md5,9d47939e48ad3a6f47a83dfc3f4cba5d", + "ribowaltz_psite_regions_mqc.tsv:md5,31c7d9a993d3203518ab2a1f66710d55", "treated_vs_control.R_sessionInfo.log:md5,9388c2a7f77dfde471cd9b67687070e4" ] ], @@ -1344,6 +1610,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-16T09:48:45.930947621" + "timestamp": "2026-01-05T13:16:48.927786718" } } \ No newline at end of file diff --git a/tests/equalise_read_lengths.nf.test.snap b/tests/equalise_read_lengths.nf.test.snap index 050a1543..115949e6 100644 --- a/tests/equalise_read_lengths.nf.test.snap +++ b/tests/equalise_read_lengths.nf.test.snap @@ -328,40 +328,47 @@ "multiqc/star", "multiqc/star/multiqc_report.html", "multiqc/star/multiqc_report_data", + "multiqc/star/multiqc_report_data/bowtie2_pe_plot.txt", + "multiqc/star/multiqc_report_data/bowtie2_se_plot.txt", "multiqc/star/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star/multiqc_report_data/fastqc-1-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc-1_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_duplication_levels_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_top_overrepresented_sequences_table.txt", - "multiqc/star/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/llms-full.txt", "multiqc/star/multiqc_report_data/multiqc.log", "multiqc/star/multiqc_report_data/multiqc.parquet", + "multiqc/star/multiqc_report_data/multiqc_bowtie2_bowtie2_rrna.txt", "multiqc/star/multiqc_report_data/multiqc_citations.txt", "multiqc/star/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star/multiqc_report_data/multiqc_data.json", - "multiqc/star/multiqc_report_data/multiqc_fastqc.txt", - "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc-1.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", "multiqc/star/multiqc_report_data/multiqc_general_stats.txt", "multiqc/star/multiqc_report_data/multiqc_ribotish.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_1_psite_regions_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_2_frames_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_3_metaprofile_start_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_4_metaprofile_stop_plot.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_stats.txt", @@ -384,35 +391,43 @@ "multiqc/star/multiqc_report_data/star_summary_table.txt", "multiqc/star/multiqc_report_plots", "multiqc/star/multiqc_report_plots/pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_pe_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_pe_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_se_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_se_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_duplication_levels_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_top_overrepresented_sequences_table.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_frame_proportions.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_read_length_line.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_1_psite_regions_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_2_frames_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_3_metaprofile_start_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_4_metaprofile_stop_plot.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -430,35 +445,43 @@ "multiqc/star/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star/multiqc_report_plots/png", + "multiqc/star/multiqc_report_plots/png/bowtie2_pe_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_pe_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_se_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_se_plot-pct.png", "multiqc/star/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_duplication_levels_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_top_overrepresented_sequences_table.png", - "multiqc/star/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/ribotish_frame_proportions.png", "multiqc/star/multiqc_report_plots/png/ribotish_read_length_line.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_1_psite_regions_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_2_frames_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_3_metaprofile_start_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_4_metaprofile_stop_plot.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-pct-table.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-table.png", "multiqc/star/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -476,35 +499,43 @@ "multiqc/star/multiqc_report_plots/png/star_alignment_plot-pct.png", "multiqc/star/multiqc_report_plots/png/star_summary_table.png", "multiqc/star/multiqc_report_plots/svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_pe_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_pe_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_se_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_se_plot-pct.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_duplication_levels_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_top_overrepresented_sequences_table.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_frame_proportions.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_read_length_line.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_1_psite_regions_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_2_frames_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_3_metaprofile_start_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_4_metaprofile_stop_plot.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -545,6 +576,32 @@ "orf_predictions/ribotish_all/allsamples_all.txt", "orf_predictions/ribotish_all/allsamples_pred.txt", "orf_predictions/ribotish_all/allsamples_transprofile.py", + "other", + "other/ribowaltz", + "other/ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780885.psite.tsv.gz", + "other/ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780886.psite.tsv.gz", + "other/ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780887.psite.tsv.gz", + "other/ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780888.psite.tsv.gz", + "other/ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780889.psite.tsv.gz", + "other/ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780890.psite.tsv.gz", "pipeline_info", "pipeline_info/nf_core_riboseq_software_mqc_versions.yml", "preprocessing", @@ -915,188 +972,211 @@ "riboseq_qc/ribotish/SRX11780890.para.py", "riboseq_qc/ribotish/SRX11780890_qual.pdf", "riboseq_qc/ribotish/SRX11780890_qual.txt", + "riboseq_qc/ribowaltz", + "riboseq_qc/ribowaltz/SRX11780885.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780885.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780886.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780886.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780887.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780887.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780888.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780888.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780889.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780889.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780890.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780890.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/offset_plot", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/35.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/36.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/37.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/38.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/39.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/40.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/41.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/33.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.tsv", "ribowaltz", - "ribowaltz/SRX11780885.best_offset.txt", - "ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780885.psite.tsv.gz", - "ribowaltz/SRX11780885.psite_offset.tsv.gz", - "ribowaltz/SRX11780886.best_offset.txt", - "ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780886.psite.tsv.gz", - "ribowaltz/SRX11780886.psite_offset.tsv.gz", - "ribowaltz/SRX11780887.best_offset.txt", - "ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780887.psite.tsv.gz", - "ribowaltz/SRX11780887.psite_offset.tsv.gz", - "ribowaltz/SRX11780888.best_offset.txt", - "ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780888.psite.tsv.gz", - "ribowaltz/SRX11780888.psite_offset.tsv.gz", - "ribowaltz/SRX11780889.best_offset.txt", - "ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780889.psite.tsv.gz", - "ribowaltz/SRX11780889.psite_offset.tsv.gz", - "ribowaltz/SRX11780890.best_offset.txt", - "ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780890.psite.tsv.gz", - "ribowaltz/SRX11780890.psite_offset.tsv.gz", - "ribowaltz/offset_plot", - "ribowaltz/offset_plot/SRX11780885", - "ribowaltz/offset_plot/SRX11780885/22.pdf", - "ribowaltz/offset_plot/SRX11780885/23.pdf", - "ribowaltz/offset_plot/SRX11780885/24.pdf", - "ribowaltz/offset_plot/SRX11780885/25.pdf", - "ribowaltz/offset_plot/SRX11780885/26.pdf", - "ribowaltz/offset_plot/SRX11780885/27.pdf", - "ribowaltz/offset_plot/SRX11780885/28.pdf", - "ribowaltz/offset_plot/SRX11780885/29.pdf", - "ribowaltz/offset_plot/SRX11780885/30.pdf", - "ribowaltz/offset_plot/SRX11780885/31.pdf", - "ribowaltz/offset_plot/SRX11780885/32.pdf", - "ribowaltz/offset_plot/SRX11780885/33.pdf", - "ribowaltz/offset_plot/SRX11780885/34.pdf", - "ribowaltz/offset_plot/SRX11780886", - "ribowaltz/offset_plot/SRX11780886/20.pdf", - "ribowaltz/offset_plot/SRX11780886/21.pdf", - "ribowaltz/offset_plot/SRX11780886/22.pdf", - "ribowaltz/offset_plot/SRX11780886/23.pdf", - "ribowaltz/offset_plot/SRX11780886/24.pdf", - "ribowaltz/offset_plot/SRX11780886/25.pdf", - "ribowaltz/offset_plot/SRX11780886/26.pdf", - "ribowaltz/offset_plot/SRX11780886/27.pdf", - "ribowaltz/offset_plot/SRX11780886/28.pdf", - "ribowaltz/offset_plot/SRX11780886/29.pdf", - "ribowaltz/offset_plot/SRX11780886/30.pdf", - "ribowaltz/offset_plot/SRX11780886/31.pdf", - "ribowaltz/offset_plot/SRX11780886/32.pdf", - "ribowaltz/offset_plot/SRX11780886/33.pdf", - "ribowaltz/offset_plot/SRX11780887", - "ribowaltz/offset_plot/SRX11780887/20.pdf", - "ribowaltz/offset_plot/SRX11780887/21.pdf", - "ribowaltz/offset_plot/SRX11780887/22.pdf", - "ribowaltz/offset_plot/SRX11780887/23.pdf", - "ribowaltz/offset_plot/SRX11780887/24.pdf", - "ribowaltz/offset_plot/SRX11780887/25.pdf", - "ribowaltz/offset_plot/SRX11780887/26.pdf", - "ribowaltz/offset_plot/SRX11780887/27.pdf", - "ribowaltz/offset_plot/SRX11780887/28.pdf", - "ribowaltz/offset_plot/SRX11780887/29.pdf", - "ribowaltz/offset_plot/SRX11780887/30.pdf", - "ribowaltz/offset_plot/SRX11780887/31.pdf", - "ribowaltz/offset_plot/SRX11780887/32.pdf", - "ribowaltz/offset_plot/SRX11780887/33.pdf", - "ribowaltz/offset_plot/SRX11780887/34.pdf", - "ribowaltz/offset_plot/SRX11780887/35.pdf", - "ribowaltz/offset_plot/SRX11780887/36.pdf", - "ribowaltz/offset_plot/SRX11780887/37.pdf", - "ribowaltz/offset_plot/SRX11780887/38.pdf", - "ribowaltz/offset_plot/SRX11780887/39.pdf", - "ribowaltz/offset_plot/SRX11780887/40.pdf", - "ribowaltz/offset_plot/SRX11780887/41.pdf", - "ribowaltz/offset_plot/SRX11780888", - "ribowaltz/offset_plot/SRX11780888/21.pdf", - "ribowaltz/offset_plot/SRX11780888/22.pdf", - "ribowaltz/offset_plot/SRX11780888/23.pdf", - "ribowaltz/offset_plot/SRX11780888/24.pdf", - "ribowaltz/offset_plot/SRX11780888/25.pdf", - "ribowaltz/offset_plot/SRX11780888/26.pdf", - "ribowaltz/offset_plot/SRX11780888/27.pdf", - "ribowaltz/offset_plot/SRX11780888/28.pdf", - "ribowaltz/offset_plot/SRX11780888/29.pdf", - "ribowaltz/offset_plot/SRX11780888/30.pdf", - "ribowaltz/offset_plot/SRX11780889", - "ribowaltz/offset_plot/SRX11780889/22.pdf", - "ribowaltz/offset_plot/SRX11780889/23.pdf", - "ribowaltz/offset_plot/SRX11780889/24.pdf", - "ribowaltz/offset_plot/SRX11780889/25.pdf", - "ribowaltz/offset_plot/SRX11780889/26.pdf", - "ribowaltz/offset_plot/SRX11780889/27.pdf", - "ribowaltz/offset_plot/SRX11780889/28.pdf", - "ribowaltz/offset_plot/SRX11780889/29.pdf", - "ribowaltz/offset_plot/SRX11780889/30.pdf", - "ribowaltz/offset_plot/SRX11780889/31.pdf", - "ribowaltz/offset_plot/SRX11780889/32.pdf", - "ribowaltz/offset_plot/SRX11780890", - "ribowaltz/offset_plot/SRX11780890/21.pdf", - "ribowaltz/offset_plot/SRX11780890/22.pdf", - "ribowaltz/offset_plot/SRX11780890/23.pdf", - "ribowaltz/offset_plot/SRX11780890/24.pdf", - "ribowaltz/offset_plot/SRX11780890/25.pdf", - "ribowaltz/offset_plot/SRX11780890/26.pdf", - "ribowaltz/offset_plot/SRX11780890/27.pdf", - "ribowaltz/offset_plot/SRX11780890/28.pdf", - "ribowaltz/offset_plot/SRX11780890/29.pdf", - "ribowaltz/offset_plot/SRX11780890/30.pdf", - "ribowaltz/offset_plot/SRX11780890/31.pdf", - "ribowaltz/offset_plot/SRX11780890/32.pdf", - "ribowaltz/offset_plot/SRX11780890/33.pdf", - "ribowaltz/ribowaltz_qc", - "ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "ribowaltz/ribowaltz_frames_mqc.tsv", + "ribowaltz/ribowaltz_metaprofile_start_mqc.json", + "ribowaltz/ribowaltz_metaprofile_stop_mqc.json", + "ribowaltz/ribowaltz_psite_regions_mqc.tsv", "translational_efficiency", "translational_efficiency/anota2seq", "translational_efficiency/anota2seq/treated_vs_control.Anota2seqDataSet.rds", @@ -1175,33 +1255,42 @@ "SRX11780890.genome.sorted.bam.idxstats:md5,3a0b29a35c233c8a44da429c0c1c4051", "SRX11780890.transcriptome.sorted.bam.flagstat:md5,87173978a2990cd5da861ad20b0b6982", "SRX11780890.transcriptome.sorted.bam.idxstats:md5,ae7f1daff6764bbc167742d19c99d587", + "bowtie2_pe_plot.txt:md5,b4dc3c205f64fed5094f56622512451b", + "bowtie2_se_plot.txt:md5,1a9cb4b686308088e524ef2b313e2f49", "cutadapt_filtered_reads_plot.txt:md5,ff95c965185e62ff5914a5c60e7a268f", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,319e9bb90c170c4b0207d644926bf69a", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,6ed5bbd0961572352d1614cc1f25f29d", - "fastqc-1-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc-1_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", - "fastqc-1_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", - "fastqc-1_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", - "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", - "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", - "fastqc-1_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", - "fastqc-1_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", - "fastqc-1_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", - "fastqc-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", - "fastqc_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", - "fastqc_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", - "fastqc_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", - "fastqc_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", - "fastqc_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", + "fastqc_raw_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", + "fastqc_raw_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,cdd555433a5c5bae529cd086512cbb69", "fastqc_sequence_length_distribution_plot.txt:md5,d3f33f3eda7927b061fc3cdec99e8f4e", - "multiqc_citations.txt:md5,fbed4cfe1e14c87bbb60e2780edb167e", + "fastqc_trimmed-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", + "fastqc_trimmed_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", + "fastqc_trimmed_top_overrepresented_sequences_table.txt:md5,18dd505c347a3faac767f31b740265d4", + "multiqc_bowtie2_bowtie2_rrna.txt:md5,3370acc7d4ccbfb2c7535f2c962449ed", + "multiqc_citations.txt:md5,1887d882cf11c0bfe29b4dd5122f3bba", "multiqc_cutadapt.txt:md5,e6031ab468a23c95b6989a6ce9e081f5", - "multiqc_fastqc.txt:md5,435f987c78b50ab1dfe18640246f580b", - "multiqc_fastqc_fastqc-1.txt:md5,c8ce8940114de9321e6de124b6cb4c18", + "multiqc_fastqc_fastqc_raw.txt:md5,435f987c78b50ab1dfe18640246f580b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,c8ce8940114de9321e6de124b6cb4c18", "multiqc_ribotish.txt:md5,21546543970095b3bcc6ab20ac0425e7", + "multiqc_ribowaltz_1_psite_regions_plot.txt:md5,0a054c20541cee8a35a98e841d828837", + "multiqc_ribowaltz_2_frames_plot.txt:md5,2d3805092494ba14f3cba0d862c34656", + "multiqc_ribowaltz_3_metaprofile_start_plot.txt:md5,4d63cc9e6fbcdac63cb222eb1c2709a9", + "multiqc_ribowaltz_4_metaprofile_stop_plot.txt:md5,dedfc06570e87423138ddf8ca9bdc23e", "multiqc_samtools_flagstat.txt:md5,59c742e509ef14bb576f7a1bdb096b13", "multiqc_samtools_idxstats.txt:md5,d36cbb3c20fa8211589bb16165e06b55", "multiqc_samtools_stats.txt:md5,76712df55faaf69b9de6415f35e4dc78", @@ -1241,6 +1330,30 @@ "allsamples_all.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_pred.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_transprofile.py:md5,51abc67be45f2a68677a551c887ff930", + "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", + "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", + "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", + "SRX11780885.psite.tsv.gz:md5,8276459cd5f05ae92510e9c983f643db", + "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", + "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", + "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", + "SRX11780886.psite.tsv.gz:md5,d5776b81cdd2af8504fc3db2041da515", + "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", + "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", + "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", + "SRX11780887.psite.tsv.gz:md5,bec9bc165cd21e17fc03a86cb87005c5", + "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", + "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", + "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", + "SRX11780888.psite.tsv.gz:md5,1e91a44a68e1918506962648d56a9192", + "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", + "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", + "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", + "SRX11780889.psite.tsv.gz:md5,df4d090347750c96c3b331dab0f582a9", + "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", + "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", + "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", + "SRX11780890.psite.tsv.gz:md5,ad3e7a4abdba33a47bfe369cd7f2a725", "SRX11780879.bowtie2.log:md5,44dd58926df16decd27314e7c42ba3b9", "SRX11780880.bowtie2.log:md5,69100acbfbda03335ba3ac7cbffdb16f", "SRX11780881.bowtie2.log:md5,99b022d64a54c14bacb95d633554e613", @@ -1322,47 +1435,200 @@ "SRX11780890.para.py:md5,5f1696c5bf20116fa63363917e131284", "SRX11780890_qual.txt:md5,0f761538ecafb2718bd781c6e1fb7dc1", "SRX11780885.best_offset.txt:md5,1e6611858fd98bf4384cb121afb6707c", - "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", - "SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,87c80db54f46aac956f46a3ae09b23bc", - "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", - "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", - "SRX11780885.psite.tsv.gz:md5,8276459cd5f05ae92510e9c983f643db", "SRX11780885.psite_offset.tsv.gz:md5,2ef8627be1603928b16f5fb561ac47b6", "SRX11780886.best_offset.txt:md5,787599a080c37b7d6eda470c13cc2563", - "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", - "SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,9b15a2401a9f0e42c060526f85596d8b", - "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", - "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", - "SRX11780886.psite.tsv.gz:md5,d5776b81cdd2af8504fc3db2041da515", "SRX11780886.psite_offset.tsv.gz:md5,583bea05a8cacd96adec469132c968f5", "SRX11780887.best_offset.txt:md5,827cbf2c4231dd868dc6f93f8b6e83b0", - "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", - "SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,4fdbeb658fd750c97873f0a2d64ec3ef", - "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", - "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", - "SRX11780887.psite.tsv.gz:md5,bec9bc165cd21e17fc03a86cb87005c5", "SRX11780887.psite_offset.tsv.gz:md5,14eebe2a609db07671c22ba4486e8d99", "SRX11780888.best_offset.txt:md5,df1bd7c66c950c943d200199d072f808", - "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", - "SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,26fb1fddeb9db9f4b46e027537af491b", - "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", - "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", - "SRX11780888.psite.tsv.gz:md5,1e91a44a68e1918506962648d56a9192", "SRX11780888.psite_offset.tsv.gz:md5,b52ce5b4cd9a95231d02fc5fed83af70", "SRX11780889.best_offset.txt:md5,d01cc2839b5415179f8f02b1fe583698", - "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", - "SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,62d1ad2c5d06dcc2f5e4b38037bac919", - "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", - "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", - "SRX11780889.psite.tsv.gz:md5,df4d090347750c96c3b331dab0f582a9", "SRX11780889.psite_offset.tsv.gz:md5,e73bb4cd13df6f92efdbaa7dcf380784", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", - "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", - "SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,e51b52241818e27eb6f194af36dfc15a", - "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", - "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", - "SRX11780890.psite.tsv.gz:md5,ad3e7a4abdba33a47bfe369cd7f2a725", "SRX11780890.psite_offset.tsv.gz:md5,4c640cbe8c24465fa1758951af308534", + "22.pdf:md5,4d77377fc70c5a99ee5031320f763331", + "23.pdf:md5,0a1f5a92e7f837fa0235b200f0b55c4f", + "24.pdf:md5,108eb01fd10a2391d8fc3770910d163c", + "25.pdf:md5,0cd2ade79fbe0e1b4bacc654a6e5bd93", + "26.pdf:md5,c51daa118e895fe1c059ade7c30edf39", + "27.pdf:md5,676d993feb1d74331df622e9f1fb336e", + "28.pdf:md5,875e1a571ffd0e6ae42f94dcb97e2f3e", + "29.pdf:md5,a244170781358fd00205557cd6ec2532", + "30.pdf:md5,f6876b3a0c6c760289407a93eea5020b", + "31.pdf:md5,eea2d82d61fe2a80fddfc956e6b5ef29", + "32.pdf:md5,b14be5294a04638b5811f17702fc6218", + "33.pdf:md5,928f2847fd34a31beb52f40829758d39", + "34.pdf:md5,c010b5b5607a0fd2cbbc7dab2ccc7851", + "20.pdf:md5,aaed45186211589d913dd53260fec69c", + "21.pdf:md5,83b07ef1807fa7db91b97e97cb1826c1", + "22.pdf:md5,7c076bc9427c8cdaedfcb799217cabb4", + "23.pdf:md5,88b08f86fb8719104dbca09e6a31efd3", + "24.pdf:md5,53b13127cf4ad6750beda0dec7b1478e", + "25.pdf:md5,d10e724fafe8f29deaddfa5e22722e11", + "26.pdf:md5,4d506d317c13ce3873a57913bc28e958", + "27.pdf:md5,42d6d32022d0ef9a909aaeb64eca3eca", + "28.pdf:md5,49badfc816cabb1e0603359a9e257582", + "29.pdf:md5,c6bf6156a05e8049d4b7bef83488c9a1", + "30.pdf:md5,ee08554286860ea3828665cef8e18779", + "31.pdf:md5,ee208971d436568c029f761f9c44b84b", + "32.pdf:md5,d2ee13efac1e005f463820dafb40c1cd", + "33.pdf:md5,a7a602a2b9031358b745e5fe4b5c17f2", + "20.pdf:md5,55bddb91f8b05ab15da8c66242eb8b7c", + "21.pdf:md5,7eec37e70d3808e633f8e65a5faaf98d", + "22.pdf:md5,a1da5f20b194b35cd3c18e7476f84d23", + "23.pdf:md5,1f5c38105ae648c7635cf2dafe181cd2", + "24.pdf:md5,2de3e6c24f375f91aef05808c527642f", + "25.pdf:md5,367e7db66dfbb8621854213a5ce90608", + "26.pdf:md5,b87e217faad8f2f3b2a7475ee5e12a4b", + "27.pdf:md5,e302d9b35d8c79c9496d8b3d091a5731", + "28.pdf:md5,e01ef4a07abde53e591b0b17c1768c93", + "29.pdf:md5,5d20a4aa4c1d0b9cc5518eb365dea534", + "30.pdf:md5,f7420fafccfad386690f0a812965a9af", + "31.pdf:md5,e4f7e57833e04d749d0834d68cc57c1b", + "32.pdf:md5,36851da54ccd4930d7d40203cf022f76", + "33.pdf:md5,55a0c5fdd667cecfe7ce688fcbea8325", + "34.pdf:md5,e6a419cd670431342bd24f7632e25f7b", + "35.pdf:md5,be5fb83df663ba29cc28c1b9f4faff96", + "36.pdf:md5,8c280df440539ab2f7d482aa84c5450f", + "37.pdf:md5,4d60a855ae6b0415c15d35bc407a1d7e", + "38.pdf:md5,bfa5f7460c02910b71c77f10e6bd07a8", + "39.pdf:md5,8d66c6887d9bf425f9b991964e28c3ff", + "40.pdf:md5,4dbc7a246a630f9cff2adc8c2c8847e5", + "41.pdf:md5,ba3b057dcb0d1e3c2fd6876da71d1856", + "21.pdf:md5,48d52a1f84d23dde50aa4adde248598d", + "22.pdf:md5,10d987cf7a4b45b82e4d425d4cd518de", + "23.pdf:md5,2d25dfe20e1debe4c6adc337a95376d7", + "24.pdf:md5,6e545bf3da967965dc8fe58f0697c3a8", + "25.pdf:md5,c22e72819436035f0e6683de47efe17d", + "26.pdf:md5,6bf9ffc3234742c670b1bc2e5e5f32b1", + "27.pdf:md5,baefb7e908384846599aca01197b385c", + "28.pdf:md5,0f3cfbe286f4d842e7a0c55280b32825", + "29.pdf:md5,8105fc12c35505429deb0a0da653a2d1", + "30.pdf:md5,4f03245910c8fc6498dd0a9c764b356d", + "22.pdf:md5,a5de6ae8ea4e88373035700387ceb790", + "23.pdf:md5,6bbccb27991fb71744aa408718c4a5e0", + "24.pdf:md5,500c763e78c4471d7d299c26d831157f", + "25.pdf:md5,57c4b3e821771f59fe8f9c6168236a3a", + "26.pdf:md5,2127e1151f0e765e537b594f3b4f0be0", + "27.pdf:md5,e74c800a16f37275f2351cb58fd5535f", + "28.pdf:md5,0105998e3598a7b432ec4dde1c0b4c0d", + "29.pdf:md5,7d807865617191a705a896d8dbc8bd3a", + "30.pdf:md5,cb084d2e3f23fad7f2c3deeca32e95e4", + "31.pdf:md5,9dbab4006b39b3c74d01455b0fb3295f", + "32.pdf:md5,0f6461c6ff9b20841864f5f2bc9092fa", + "21.pdf:md5,a000b48ed1199ed6787afe15a1ee0a88", + "22.pdf:md5,0341d4ab1bde04d742ff89976dca5dce", + "23.pdf:md5,43f5f320f2bb043b78d5c54d305f489c", + "24.pdf:md5,d57b502a396df03709f5195ff7f546de", + "25.pdf:md5,1bc06a5266926eaccbcfdb2f84cd1ef8", + "26.pdf:md5,854ee9abc2efe783d8326128ed85f500", + "27.pdf:md5,23af7d0cf71e61ddd6c61cd33221a679", + "28.pdf:md5,a2b1274dd44b3903bb4f74dd31f8d835", + "29.pdf:md5,01015d7c5adf7e68b9db2b258a1ffe12", + "30.pdf:md5,0e254679b7af776ac7f5adde4dc39d01", + "31.pdf:md5,d51c9c26731930f6bb1b13f272afabdb", + "32.pdf:md5,8505b7f0d502eccfd185b955faf7be58", + "33.pdf:md5,44d4335c375b3792838fa6273cc53676", + "SRX11780885.codon_usage.pdf:md5,1f42417b18e7874eb9eba22b0dbf760d", + "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", + "SRX11780885.ends_heatmap.pdf:md5,b219cd10f89cead5846e87e7be0ec896", + "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", + "SRX11780885.frames.pdf:md5,df9c8981c10e9ef21165d123d66623b3", + "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", + "SRX11780885.frames_stratified.pdf:md5,2476b7e6b72eabe2a5b0b86cdd37d5d5", + "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", + "SRX11780885.length_bins_for_psite.pdf:md5,ead05e694d3944242f73245b3d34bdd0", + "SRX11780885.length_bins_for_psite.tsv:md5,b6fd5abd7f639276df10698b94d3cc52", + "SRX11780885.length_distribution.pdf:md5,6a9706e257edc17555cab4598b7618e4", + "SRX11780885.length_distribution.tsv:md5,82bee1b71c13feb716f000d4982ed3cf", + "SRX11780885.metaprofile_psite.pdf:md5,b7a404bd68a952179606d5ef75c55bec", + "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", + "SRX11780885.psite_region.pdf:md5,5914175cb5d9654a740cabfbf5b77e43", + "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", + "SRX11780886.codon_usage.pdf:md5,6baa919d0076e209df880671719b1d06", + "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", + "SRX11780886.ends_heatmap.pdf:md5,f366b705f84135b9f9904830a2fb5897", + "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", + "SRX11780886.frames.pdf:md5,aac90230bd23cdf9c7fa343d3bc96404", + "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", + "SRX11780886.frames_stratified.pdf:md5,0926e983558de72f0ecc6cf4fdf4097d", + "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", + "SRX11780886.length_bins_for_psite.pdf:md5,c9f4e24cc683e8e66b0310ef5dfb542a", + "SRX11780886.length_bins_for_psite.tsv:md5,e226199778c919ad4da4d6ff39379742", + "SRX11780886.length_distribution.pdf:md5,1e5b58fc380bb39aca855ddcd4f8961b", + "SRX11780886.length_distribution.tsv:md5,b272c92a918a405b2cccba30ff0405e1", + "SRX11780886.metaprofile_psite.pdf:md5,a7c5af8e75cbc531a9c004a7b915b047", + "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", + "SRX11780886.psite_region.pdf:md5,8407ad9b1f38da6189b5d2c4fa354ac3", + "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", + "SRX11780887.codon_usage.pdf:md5,e1229b40fa024648fddef9eceb4c8088", + "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", + "SRX11780887.ends_heatmap.pdf:md5,3fe0e4375c96792928aae1f01f525406", + "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", + "SRX11780887.frames.pdf:md5,c3bf11e1ccc7d05006fdbcc27378ef92", + "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", + "SRX11780887.frames_stratified.pdf:md5,72677d4a6793c7cf4769f8ded71602bd", + "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", + "SRX11780887.length_bins_for_psite.pdf:md5,5c3a81293bff96761d83963edad16330", + "SRX11780887.length_bins_for_psite.tsv:md5,545a6874f9f3d82c26f28b04977dfcb8", + "SRX11780887.length_distribution.pdf:md5,57c47fb920aa893166333da87f2d11c2", + "SRX11780887.length_distribution.tsv:md5,ce512154c88e9cee2c2a9509f82918e8", + "SRX11780887.metaprofile_psite.pdf:md5,f3286226dfa230aa23d4acc3293add79", + "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", + "SRX11780887.psite_region.pdf:md5,feb1e24772ca172f29f9414d0ef7d617", + "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", + "SRX11780888.codon_usage.pdf:md5,3df7a37e3979f41b4e117021a369e47a", + "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", + "SRX11780888.ends_heatmap.pdf:md5,83b2490dacae8101706579ea7a0082f0", + "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", + "SRX11780888.frames.pdf:md5,f59945fbfea29500063a3351fa807f64", + "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", + "SRX11780888.frames_stratified.pdf:md5,c2e3289cb3a39fe4e63a62a0b17ac654", + "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", + "SRX11780888.length_bins_for_psite.pdf:md5,241fa1807c496bf0ea7e11a07628363c", + "SRX11780888.length_bins_for_psite.tsv:md5,f7d9223b388a77dd91c5a41aa89134c7", + "SRX11780888.length_distribution.pdf:md5,bf45db12cffcf99eb981abb221adc0ca", + "SRX11780888.length_distribution.tsv:md5,3e5ef7ee2e090123cf4c2bc6ea71bb01", + "SRX11780888.metaprofile_psite.pdf:md5,b84b2409905f3cb4d5af7f7b011dfb5d", + "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", + "SRX11780888.psite_region.pdf:md5,ccc610c32d8fc22b5a2957d11bfd6416", + "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", + "SRX11780889.codon_usage.pdf:md5,c9f9e86adb274b15058482310381b1ee", + "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", + "SRX11780889.ends_heatmap.pdf:md5,a07d4c583b1eb40bc149c6597592671b", + "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", + "SRX11780889.frames.pdf:md5,090c99de1f712453885a5e35676834fe", + "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", + "SRX11780889.frames_stratified.pdf:md5,fcbbd9a9b7ad1fef62ffa20f23a57d4e", + "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", + "SRX11780889.length_bins_for_psite.pdf:md5,66133c97ebcaf77c37473b4e89a41d05", + "SRX11780889.length_bins_for_psite.tsv:md5,488b91e071d8bcd3d8933974bd6cf952", + "SRX11780889.length_distribution.pdf:md5,34c8a52ae0401bf7b06a31820264ed91", + "SRX11780889.length_distribution.tsv:md5,cc5ae4ad914c8afba7726dccc47f9cd0", + "SRX11780889.metaprofile_psite.pdf:md5,aa531c475e4d18ab6c9fc84c2926e863", + "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", + "SRX11780889.psite_region.pdf:md5,5d65b6d9a1c2878c95893018104d405b", + "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", + "SRX11780890.codon_usage.pdf:md5,e5c4e21daee6d4536cc5e7241bf1f4dc", + "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", + "SRX11780890.ends_heatmap.pdf:md5,a55d2db23a04d20848cfb5d0384a0478", + "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", + "SRX11780890.frames.pdf:md5,8bc7b7355335035bf52692cac9575943", + "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", + "SRX11780890.frames_stratified.pdf:md5,ef1909d5da303ea57ae5c1355d8f9207", + "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", + "SRX11780890.length_bins_for_psite.pdf:md5,dde92c874794d79570fe244cba1d54f3", + "SRX11780890.length_bins_for_psite.tsv:md5,5bed6cd6fb8f944a6e0e7d9325dce6c3", + "SRX11780890.length_distribution.pdf:md5,7263a40fb1b7ef1e0b5614a20f0e7579", + "SRX11780890.length_distribution.tsv:md5,2ee60618861bde90a7ebcbba7013adfe", + "SRX11780890.metaprofile_psite.pdf:md5,e4b4442baaaf399c1d29c2c4b871df1e", + "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", + "SRX11780890.psite_region.pdf:md5,26ccb8626b4b103b16704f08394fc6c5", + "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", + "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", + "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8", + "ribowaltz_metaprofile_stop_mqc.json:md5,9d47939e48ad3a6f47a83dfc3f4cba5d", + "ribowaltz_psite_regions_mqc.tsv:md5,31c7d9a993d3203518ab2a1f66710d55", "treated_vs_control.R_sessionInfo.log:md5,3623a50b4668bfebf502bf7080800996" ] ], @@ -1370,6 +1636,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-16T17:58:51.260115235" + "timestamp": "2026-01-05T13:25:45.179894929" } } \ No newline at end of file diff --git a/tests/ribo_removal_bowtie2.nf.test.snap b/tests/ribo_removal_bowtie2.nf.test.snap index 170c690a..b0ba5aff 100644 --- a/tests/ribo_removal_bowtie2.nf.test.snap +++ b/tests/ribo_removal_bowtie2.nf.test.snap @@ -320,40 +320,47 @@ "multiqc/star", "multiqc/star/multiqc_report.html", "multiqc/star/multiqc_report_data", + "multiqc/star/multiqc_report_data/bowtie2_pe_plot.txt", + "multiqc/star/multiqc_report_data/bowtie2_se_plot.txt", "multiqc/star/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star/multiqc_report_data/fastqc-1-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc-1_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc-1_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_sequence_duplication_levels_plot.txt", - "multiqc/star/multiqc_report_data/fastqc-1_top_overrepresented_sequences_table.txt", - "multiqc/star/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star/multiqc_report_data/llms-full.txt", "multiqc/star/multiqc_report_data/multiqc.log", "multiqc/star/multiqc_report_data/multiqc.parquet", + "multiqc/star/multiqc_report_data/multiqc_bowtie2_bowtie2_rrna.txt", "multiqc/star/multiqc_report_data/multiqc_citations.txt", "multiqc/star/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star/multiqc_report_data/multiqc_data.json", - "multiqc/star/multiqc_report_data/multiqc_fastqc.txt", - "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc-1.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", "multiqc/star/multiqc_report_data/multiqc_general_stats.txt", "multiqc/star/multiqc_report_data/multiqc_ribotish.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_1_psite_regions_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_2_frames_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_3_metaprofile_start_plot.txt", + "multiqc/star/multiqc_report_data/multiqc_ribowaltz_4_metaprofile_stop_plot.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star/multiqc_report_data/multiqc_samtools_stats.txt", @@ -373,35 +380,43 @@ "multiqc/star/multiqc_report_data/star_summary_table.txt", "multiqc/star/multiqc_report_plots", "multiqc/star/multiqc_report_plots/pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_pe_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_pe_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_se_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/bowtie2_se_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_sequence_duplication_levels_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-1_top_overrepresented_sequences_table.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_frame_proportions.pdf", "multiqc/star/multiqc_report_plots/pdf/ribotish_read_length_line.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_1_psite_regions_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_2_frames_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_3_metaprofile_start_plot.pdf", + "multiqc/star/multiqc_report_plots/pdf/ribowaltz_4_metaprofile_stop_plot.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-flagstat-table.pdf", "multiqc/star/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -417,35 +432,43 @@ "multiqc/star/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", "multiqc/star/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star/multiqc_report_plots/png", + "multiqc/star/multiqc_report_plots/png/bowtie2_pe_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_pe_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_se_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/bowtie2_se_plot-pct.png", "multiqc/star/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_sequence_duplication_levels_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc-1_top_overrepresented_sequences_table.png", - "multiqc/star/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star/multiqc_report_plots/png/ribotish_frame_proportions.png", "multiqc/star/multiqc_report_plots/png/ribotish_read_length_line.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_1_psite_regions_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_2_frames_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_3_metaprofile_start_plot.png", + "multiqc/star/multiqc_report_plots/png/ribowaltz_4_metaprofile_stop_plot.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-pct-table.png", "multiqc/star/multiqc_report_plots/png/samtools-flagstat-table.png", "multiqc/star/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -461,35 +484,43 @@ "multiqc/star/multiqc_report_plots/png/star_alignment_plot-pct.png", "multiqc/star/multiqc_report_plots/png/star_summary_table.png", "multiqc/star/multiqc_report_plots/svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_pe_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_pe_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_se_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/bowtie2_se_plot-pct.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_sequence_duplication_levels_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-1_top_overrepresented_sequences_table.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_frame_proportions.svg", "multiqc/star/multiqc_report_plots/svg/ribotish_read_length_line.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_1_psite_regions_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_2_frames_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_3_metaprofile_start_plot.svg", + "multiqc/star/multiqc_report_plots/svg/ribowaltz_4_metaprofile_stop_plot.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-flagstat-table.svg", "multiqc/star/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -528,6 +559,32 @@ "orf_predictions/ribotish_all/allsamples_all.txt", "orf_predictions/ribotish_all/allsamples_pred.txt", "orf_predictions/ribotish_all/allsamples_transprofile.py", + "other", + "other/ribowaltz", + "other/ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780885.psite.tsv.gz", + "other/ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780886.psite.tsv.gz", + "other/ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780887.psite.tsv.gz", + "other/ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780888.psite.tsv.gz", + "other/ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780889.psite.tsv.gz", + "other/ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", + "other/ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", + "other/ribowaltz/SRX11780890.psite.tsv.gz", "pipeline_info", "pipeline_info/nf_core_riboseq_software_mqc_versions.yml", "preprocessing", @@ -890,188 +947,211 @@ "riboseq_qc/ribotish/SRX11780890.para.py", "riboseq_qc/ribotish/SRX11780890_qual.pdf", "riboseq_qc/ribotish/SRX11780890_qual.txt", + "riboseq_qc/ribowaltz", + "riboseq_qc/ribowaltz/SRX11780885.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780885.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780886.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780886.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780887.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780887.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780888.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780888.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780889.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780889.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/SRX11780890.best_offset.txt", + "riboseq_qc/ribowaltz/SRX11780890.psite_offset.tsv.gz", + "riboseq_qc/ribowaltz/offset_plot", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780885/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780886/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/20.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/33.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/34.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/35.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/36.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/37.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/38.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/39.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/40.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780887/41.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780888/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780889/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/21.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/22.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/23.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/24.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/25.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/26.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/27.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/28.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/29.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/30.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/31.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/32.pdf", + "riboseq_qc/ribowaltz/offset_plot/SRX11780890/33.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780885.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780886.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780887.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780888.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780889.psite_region.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.tsv", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "riboseq_qc/ribowaltz/ribowaltz_qc/SRX11780890.psite_region.tsv", "ribowaltz", - "ribowaltz/SRX11780885.best_offset.txt", - "ribowaltz/SRX11780885.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780885.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780885.psite.tsv.gz", - "ribowaltz/SRX11780885.psite_offset.tsv.gz", - "ribowaltz/SRX11780886.best_offset.txt", - "ribowaltz/SRX11780886.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780886.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780886.psite.tsv.gz", - "ribowaltz/SRX11780886.psite_offset.tsv.gz", - "ribowaltz/SRX11780887.best_offset.txt", - "ribowaltz/SRX11780887.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780887.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780887.psite.tsv.gz", - "ribowaltz/SRX11780887.psite_offset.tsv.gz", - "ribowaltz/SRX11780888.best_offset.txt", - "ribowaltz/SRX11780888.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780888.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780888.psite.tsv.gz", - "ribowaltz/SRX11780888.psite_offset.tsv.gz", - "ribowaltz/SRX11780889.best_offset.txt", - "ribowaltz/SRX11780889.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780889.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780889.psite.tsv.gz", - "ribowaltz/SRX11780889.psite_offset.tsv.gz", - "ribowaltz/SRX11780890.best_offset.txt", - "ribowaltz/SRX11780890.cds_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_psite.tsv.gz", - "ribowaltz/SRX11780890.codon_coverage_rpf.tsv.gz", - "ribowaltz/SRX11780890.psite.tsv.gz", - "ribowaltz/SRX11780890.psite_offset.tsv.gz", - "ribowaltz/offset_plot", - "ribowaltz/offset_plot/SRX11780885", - "ribowaltz/offset_plot/SRX11780885/22.pdf", - "ribowaltz/offset_plot/SRX11780885/23.pdf", - "ribowaltz/offset_plot/SRX11780885/24.pdf", - "ribowaltz/offset_plot/SRX11780885/25.pdf", - "ribowaltz/offset_plot/SRX11780885/26.pdf", - "ribowaltz/offset_plot/SRX11780885/27.pdf", - "ribowaltz/offset_plot/SRX11780885/28.pdf", - "ribowaltz/offset_plot/SRX11780885/29.pdf", - "ribowaltz/offset_plot/SRX11780885/30.pdf", - "ribowaltz/offset_plot/SRX11780885/31.pdf", - "ribowaltz/offset_plot/SRX11780885/32.pdf", - "ribowaltz/offset_plot/SRX11780885/33.pdf", - "ribowaltz/offset_plot/SRX11780885/34.pdf", - "ribowaltz/offset_plot/SRX11780886", - "ribowaltz/offset_plot/SRX11780886/20.pdf", - "ribowaltz/offset_plot/SRX11780886/21.pdf", - "ribowaltz/offset_plot/SRX11780886/22.pdf", - "ribowaltz/offset_plot/SRX11780886/23.pdf", - "ribowaltz/offset_plot/SRX11780886/24.pdf", - "ribowaltz/offset_plot/SRX11780886/25.pdf", - "ribowaltz/offset_plot/SRX11780886/26.pdf", - "ribowaltz/offset_plot/SRX11780886/27.pdf", - "ribowaltz/offset_plot/SRX11780886/28.pdf", - "ribowaltz/offset_plot/SRX11780886/29.pdf", - "ribowaltz/offset_plot/SRX11780886/30.pdf", - "ribowaltz/offset_plot/SRX11780886/31.pdf", - "ribowaltz/offset_plot/SRX11780886/32.pdf", - "ribowaltz/offset_plot/SRX11780886/33.pdf", - "ribowaltz/offset_plot/SRX11780887", - "ribowaltz/offset_plot/SRX11780887/20.pdf", - "ribowaltz/offset_plot/SRX11780887/21.pdf", - "ribowaltz/offset_plot/SRX11780887/22.pdf", - "ribowaltz/offset_plot/SRX11780887/23.pdf", - "ribowaltz/offset_plot/SRX11780887/24.pdf", - "ribowaltz/offset_plot/SRX11780887/25.pdf", - "ribowaltz/offset_plot/SRX11780887/26.pdf", - "ribowaltz/offset_plot/SRX11780887/27.pdf", - "ribowaltz/offset_plot/SRX11780887/28.pdf", - "ribowaltz/offset_plot/SRX11780887/29.pdf", - "ribowaltz/offset_plot/SRX11780887/30.pdf", - "ribowaltz/offset_plot/SRX11780887/31.pdf", - "ribowaltz/offset_plot/SRX11780887/32.pdf", - "ribowaltz/offset_plot/SRX11780887/33.pdf", - "ribowaltz/offset_plot/SRX11780887/34.pdf", - "ribowaltz/offset_plot/SRX11780887/35.pdf", - "ribowaltz/offset_plot/SRX11780887/36.pdf", - "ribowaltz/offset_plot/SRX11780887/37.pdf", - "ribowaltz/offset_plot/SRX11780887/38.pdf", - "ribowaltz/offset_plot/SRX11780887/39.pdf", - "ribowaltz/offset_plot/SRX11780887/40.pdf", - "ribowaltz/offset_plot/SRX11780887/41.pdf", - "ribowaltz/offset_plot/SRX11780888", - "ribowaltz/offset_plot/SRX11780888/21.pdf", - "ribowaltz/offset_plot/SRX11780888/22.pdf", - "ribowaltz/offset_plot/SRX11780888/23.pdf", - "ribowaltz/offset_plot/SRX11780888/24.pdf", - "ribowaltz/offset_plot/SRX11780888/25.pdf", - "ribowaltz/offset_plot/SRX11780888/26.pdf", - "ribowaltz/offset_plot/SRX11780888/27.pdf", - "ribowaltz/offset_plot/SRX11780888/28.pdf", - "ribowaltz/offset_plot/SRX11780888/29.pdf", - "ribowaltz/offset_plot/SRX11780888/30.pdf", - "ribowaltz/offset_plot/SRX11780889", - "ribowaltz/offset_plot/SRX11780889/22.pdf", - "ribowaltz/offset_plot/SRX11780889/23.pdf", - "ribowaltz/offset_plot/SRX11780889/24.pdf", - "ribowaltz/offset_plot/SRX11780889/25.pdf", - "ribowaltz/offset_plot/SRX11780889/26.pdf", - "ribowaltz/offset_plot/SRX11780889/27.pdf", - "ribowaltz/offset_plot/SRX11780889/28.pdf", - "ribowaltz/offset_plot/SRX11780889/29.pdf", - "ribowaltz/offset_plot/SRX11780889/30.pdf", - "ribowaltz/offset_plot/SRX11780889/31.pdf", - "ribowaltz/offset_plot/SRX11780889/32.pdf", - "ribowaltz/offset_plot/SRX11780890", - "ribowaltz/offset_plot/SRX11780890/21.pdf", - "ribowaltz/offset_plot/SRX11780890/22.pdf", - "ribowaltz/offset_plot/SRX11780890/23.pdf", - "ribowaltz/offset_plot/SRX11780890/24.pdf", - "ribowaltz/offset_plot/SRX11780890/25.pdf", - "ribowaltz/offset_plot/SRX11780890/26.pdf", - "ribowaltz/offset_plot/SRX11780890/27.pdf", - "ribowaltz/offset_plot/SRX11780890/28.pdf", - "ribowaltz/offset_plot/SRX11780890/29.pdf", - "ribowaltz/offset_plot/SRX11780890/30.pdf", - "ribowaltz/offset_plot/SRX11780890/31.pdf", - "ribowaltz/offset_plot/SRX11780890/32.pdf", - "ribowaltz/offset_plot/SRX11780890/33.pdf", - "ribowaltz/ribowaltz_qc", - "ribowaltz/ribowaltz_qc/SRX11780885.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780885.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780886.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780887.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780888.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780889.psite_region.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.codon_usage.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.ends_heatmap.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.frames_stratified.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_bins_for_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.length_distribution.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.metaprofile_psite.pdf", - "ribowaltz/ribowaltz_qc/SRX11780890.psite_region.pdf", + "ribowaltz/ribowaltz_frames_mqc.tsv", + "ribowaltz/ribowaltz_metaprofile_start_mqc.json", + "ribowaltz/ribowaltz_metaprofile_stop_mqc.json", + "ribowaltz/ribowaltz_psite_regions_mqc.tsv", "translational_efficiency", "translational_efficiency/anota2seq", "translational_efficiency/anota2seq/treated_vs_control.Anota2seqDataSet.rds", @@ -1150,33 +1230,42 @@ "SRX11780890.genome.sorted.bam.idxstats:md5,3a0b29a35c233c8a44da429c0c1c4051", "SRX11780890.transcriptome.sorted.bam.flagstat:md5,87173978a2990cd5da861ad20b0b6982", "SRX11780890.transcriptome.sorted.bam.idxstats:md5,ae7f1daff6764bbc167742d19c99d587", + "bowtie2_pe_plot.txt:md5,b4dc3c205f64fed5094f56622512451b", + "bowtie2_se_plot.txt:md5,1a9cb4b686308088e524ef2b313e2f49", "cutadapt_filtered_reads_plot.txt:md5,ff95c965185e62ff5914a5c60e7a268f", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,319e9bb90c170c4b0207d644926bf69a", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,6ed5bbd0961572352d1614cc1f25f29d", - "fastqc-1-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc-1_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", - "fastqc-1_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", - "fastqc-1_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", - "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", - "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", - "fastqc-1_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", - "fastqc-1_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", - "fastqc-1_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", - "fastqc-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", - "fastqc_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", - "fastqc_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", - "fastqc_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", - "fastqc_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", - "fastqc_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", - "fastqc_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,ba7c244b0a7cd7f591b8493f2927ea7d", + "fastqc_raw_per_base_n_content_plot.txt:md5,ec70b184c102884d089ebcca0cac7216", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,c8af81414843457b45cd1dfe83c49433", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,47955155853de1e04ca812820b8fee8c", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,0e78eba9f1b8f63f5388c7078c41b302", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,609c48f48499de206085509d4dd29b8a", + "fastqc_raw_sequence_counts_plot.txt:md5,cbb44b6eb726b00e041237476214b275", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,77d6e3d36b8c93f25e2d4cdbadd018d3", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,cdd555433a5c5bae529cd086512cbb69", "fastqc_sequence_length_distribution_plot.txt:md5,d3f33f3eda7927b061fc3cdec99e8f4e", - "multiqc_citations.txt:md5,639700223364dc6a161895ecdb029710", + "fastqc_trimmed-status-check-heatmap.txt:md5,a0e26481ceebf69ed7540a8e103526aa", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,955f7e738937929fc26aba2de54ca404", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,fa8a68d48b6776dc76645fa412d06490", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,f98b44d67d52434ea97e243cefe3e080", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,9a973946f1692516940ab3f5efea44ce", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,3b4c25caf665d95a61ae8dd5e9bae84a", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,c5366f0520a574d6749ef03e9e748aa2", + "fastqc_trimmed_sequence_counts_plot.txt:md5,07490905b4b62f87d92c26f792eef7a0", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,8f7b7d1921ed8b6302196876dd36a3f5", + "fastqc_trimmed_top_overrepresented_sequences_table.txt:md5,18dd505c347a3faac767f31b740265d4", + "multiqc_bowtie2_bowtie2_rrna.txt:md5,3370acc7d4ccbfb2c7535f2c962449ed", + "multiqc_citations.txt:md5,e2b5d6b0dcf0f2e6cd2771fa8cb7039a", "multiqc_cutadapt.txt:md5,e6031ab468a23c95b6989a6ce9e081f5", - "multiqc_fastqc.txt:md5,435f987c78b50ab1dfe18640246f580b", - "multiqc_fastqc_fastqc-1.txt:md5,c8ce8940114de9321e6de124b6cb4c18", + "multiqc_fastqc_fastqc_raw.txt:md5,435f987c78b50ab1dfe18640246f580b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,c8ce8940114de9321e6de124b6cb4c18", "multiqc_ribotish.txt:md5,21546543970095b3bcc6ab20ac0425e7", + "multiqc_ribowaltz_1_psite_regions_plot.txt:md5,0a054c20541cee8a35a98e841d828837", + "multiqc_ribowaltz_2_frames_plot.txt:md5,2d3805092494ba14f3cba0d862c34656", + "multiqc_ribowaltz_3_metaprofile_start_plot.txt:md5,4d63cc9e6fbcdac63cb222eb1c2709a9", + "multiqc_ribowaltz_4_metaprofile_stop_plot.txt:md5,dedfc06570e87423138ddf8ca9bdc23e", "multiqc_samtools_flagstat.txt:md5,9fc0f9e799ae50c4b353b70aa1748b43", "multiqc_samtools_idxstats.txt:md5,acc2f751f8006c65cac9f52e5d408a2b", "multiqc_samtools_stats.txt:md5,086c61cbb732ee1ea68bbd10760dd33f", @@ -1213,6 +1302,30 @@ "allsamples_all.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_pred.txt:md5,fcdb19d5389596185db2ebce2663cd94", "allsamples_transprofile.py:md5,51abc67be45f2a68677a551c887ff930", + "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", + "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", + "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", + "SRX11780885.psite.tsv.gz:md5,8276459cd5f05ae92510e9c983f643db", + "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", + "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", + "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", + "SRX11780886.psite.tsv.gz:md5,d5776b81cdd2af8504fc3db2041da515", + "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", + "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", + "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", + "SRX11780887.psite.tsv.gz:md5,bec9bc165cd21e17fc03a86cb87005c5", + "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", + "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", + "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", + "SRX11780888.psite.tsv.gz:md5,1e91a44a68e1918506962648d56a9192", + "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", + "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", + "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", + "SRX11780889.psite.tsv.gz:md5,df4d090347750c96c3b331dab0f582a9", + "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", + "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", + "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", + "SRX11780890.psite.tsv.gz:md5,ad3e7a4abdba33a47bfe369cd7f2a725", "SRX11780879.bowtie2.log:md5,44dd58926df16decd27314e7c42ba3b9", "SRX11780880.bowtie2.log:md5,69100acbfbda03335ba3ac7cbffdb16f", "SRX11780881.bowtie2.log:md5,99b022d64a54c14bacb95d633554e613", @@ -1288,47 +1401,200 @@ "SRX11780890.para.py:md5,5f1696c5bf20116fa63363917e131284", "SRX11780890_qual.txt:md5,0f761538ecafb2718bd781c6e1fb7dc1", "SRX11780885.best_offset.txt:md5,1e6611858fd98bf4384cb121afb6707c", - "SRX11780885.cds_coverage_psite.tsv.gz:md5,f9d49b4c82a8b3e5b521441e9df4cc86", - "SRX11780885.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,87c80db54f46aac956f46a3ae09b23bc", - "SRX11780885.codon_coverage_psite.tsv.gz:md5,8a759875e7dbbf39d3720f732713678a", - "SRX11780885.codon_coverage_rpf.tsv.gz:md5,afbf801cb1ba85f404978098e572901d", - "SRX11780885.psite.tsv.gz:md5,8276459cd5f05ae92510e9c983f643db", "SRX11780885.psite_offset.tsv.gz:md5,2ef8627be1603928b16f5fb561ac47b6", "SRX11780886.best_offset.txt:md5,787599a080c37b7d6eda470c13cc2563", - "SRX11780886.cds_coverage_psite.tsv.gz:md5,3f9a35c6f34c0db4754e8a1662faa0b5", - "SRX11780886.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,9b15a2401a9f0e42c060526f85596d8b", - "SRX11780886.codon_coverage_psite.tsv.gz:md5,7aec8c79793692acd49c7858bce2b579", - "SRX11780886.codon_coverage_rpf.tsv.gz:md5,3e50a00b6520665c165e4c3fce19e5f1", - "SRX11780886.psite.tsv.gz:md5,d5776b81cdd2af8504fc3db2041da515", "SRX11780886.psite_offset.tsv.gz:md5,583bea05a8cacd96adec469132c968f5", "SRX11780887.best_offset.txt:md5,827cbf2c4231dd868dc6f93f8b6e83b0", - "SRX11780887.cds_coverage_psite.tsv.gz:md5,d7f669652ce332ab4ebcb742a72dfcf2", - "SRX11780887.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,4fdbeb658fd750c97873f0a2d64ec3ef", - "SRX11780887.codon_coverage_psite.tsv.gz:md5,770a832bc98809a2c6ee4250dab64731", - "SRX11780887.codon_coverage_rpf.tsv.gz:md5,56e1fad3c99f046eddb6fba8d8788ce9", - "SRX11780887.psite.tsv.gz:md5,bec9bc165cd21e17fc03a86cb87005c5", "SRX11780887.psite_offset.tsv.gz:md5,14eebe2a609db07671c22ba4486e8d99", "SRX11780888.best_offset.txt:md5,df1bd7c66c950c943d200199d072f808", - "SRX11780888.cds_coverage_psite.tsv.gz:md5,90e082f11c75a08d17bbd3eba354b6c1", - "SRX11780888.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,26fb1fddeb9db9f4b46e027537af491b", - "SRX11780888.codon_coverage_psite.tsv.gz:md5,1053bfe91da54816c224a897ac7226d2", - "SRX11780888.codon_coverage_rpf.tsv.gz:md5,bbd3e94215437a9d89bf61a3bfd5d49f", - "SRX11780888.psite.tsv.gz:md5,1e91a44a68e1918506962648d56a9192", "SRX11780888.psite_offset.tsv.gz:md5,b52ce5b4cd9a95231d02fc5fed83af70", "SRX11780889.best_offset.txt:md5,d01cc2839b5415179f8f02b1fe583698", - "SRX11780889.cds_coverage_psite.tsv.gz:md5,e4f51321acf53ea0610e89fe1f718759", - "SRX11780889.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,62d1ad2c5d06dcc2f5e4b38037bac919", - "SRX11780889.codon_coverage_psite.tsv.gz:md5,41ff3b1b94ed30b310bf62d110c1b671", - "SRX11780889.codon_coverage_rpf.tsv.gz:md5,0365460ff32f54ef97582566cd41803a", - "SRX11780889.psite.tsv.gz:md5,df4d090347750c96c3b331dab0f582a9", "SRX11780889.psite_offset.tsv.gz:md5,e73bb4cd13df6f92efdbaa7dcf380784", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", - "SRX11780890.cds_coverage_psite.tsv.gz:md5,ed927c97e107476fc1b86b6af1a10e27", - "SRX11780890.cds_plus42nt_minus27nt_coverage_psite.tsv.gz:md5,e51b52241818e27eb6f194af36dfc15a", - "SRX11780890.codon_coverage_psite.tsv.gz:md5,948e954e45f3f4beb19b0aa1adc384b2", - "SRX11780890.codon_coverage_rpf.tsv.gz:md5,fc28b1c4b672c3f94111a27392a0fa9c", - "SRX11780890.psite.tsv.gz:md5,ad3e7a4abdba33a47bfe369cd7f2a725", "SRX11780890.psite_offset.tsv.gz:md5,4c640cbe8c24465fa1758951af308534", + "22.pdf:md5,9430ce83ba88bfc063e992daae84683a", + "23.pdf:md5,cfdd0bb8e97edb2da7ff95f8571b1182", + "24.pdf:md5,d0872557899188349e07f243dd3f9185", + "25.pdf:md5,c8c03094cfd3fc44c72ca2f0a0f609a1", + "26.pdf:md5,4ff638511158fc6320578c69da6a786e", + "27.pdf:md5,0ba0812644e28dccb9ef8e7f28784719", + "28.pdf:md5,2718e7c79f61411a9f5e35b77cfe7481", + "29.pdf:md5,4c0b358c35e8306ef81e529340e7a6a3", + "30.pdf:md5,41a42232ae2c2fff761c9675b0977b77", + "31.pdf:md5,f6fbb51974b1e0fd52eb7565c9f6ba22", + "32.pdf:md5,4b83c011ba89a5ef6c4779d72fa35443", + "33.pdf:md5,eae09a0f37537bb3b2a12ab8dfe51761", + "34.pdf:md5,64aa815dd2ae738b61a6a751baa82847", + "20.pdf:md5,6ad3d5b7a52606656faa097bc5a94e78", + "21.pdf:md5,d686c13b1b6fbf38ef79e15fb68e8710", + "22.pdf:md5,8d10f224c0f94d4a9c5e33dc9620654f", + "23.pdf:md5,f63ea21962391bf49948670fcc568385", + "24.pdf:md5,4331bd8e1d7430f6baaaadb1d266a374", + "25.pdf:md5,91abeea6ea8c92d16ebb5bf815b96c73", + "26.pdf:md5,9fb35420cb066be5b32b40b7cc598cef", + "27.pdf:md5,9677f167e9ab3825ca243811e02d7415", + "28.pdf:md5,4b544c83d9f990dfb114f6652593d42a", + "29.pdf:md5,b404f950b012e39f5bcb4b7e925b7d96", + "30.pdf:md5,dcd7cfad1dc0144ec59e140199e51722", + "31.pdf:md5,7f6d165553ee660447a7aa6829ec8b44", + "32.pdf:md5,a1c316880a9ed2a6f6c5149a1199b816", + "33.pdf:md5,922bc7e0d1a93cf084e05d5562bb9fb6", + "20.pdf:md5,e7f22dcdb762f266a6c7e04c0b99547e", + "21.pdf:md5,f5200c024e444d346b954ed4eecccebe", + "22.pdf:md5,bb1727b4af2e776ef94b99f5e34ac07c", + "23.pdf:md5,b81663f5e0020cb19b394ea566aa55c9", + "24.pdf:md5,e181e89de74303e7ebb71c82b7c609f8", + "25.pdf:md5,1c900876f445d0bc185bc0b87345132b", + "26.pdf:md5,03c14a2842d2925db112d4c6dfd4fc1a", + "27.pdf:md5,e22f1afd5403fe1c24fb7695cc57d40e", + "28.pdf:md5,e40599ee64d6d2798623f4700277d65e", + "29.pdf:md5,850ace11533bcc418718ec7d864de333", + "30.pdf:md5,33ba00de338cd3c903fa3cf1cac45089", + "31.pdf:md5,39053ccd8e87cecc654324664c3a2d68", + "32.pdf:md5,e355e0868bed871796a494761515fdc5", + "33.pdf:md5,7808e1f34ca19f78b1af08e69033d0b4", + "34.pdf:md5,21d75e2a3692ad72cffd0adc5469c165", + "35.pdf:md5,512771f3d5712c76b615ea279cbecff8", + "36.pdf:md5,815515d31127f482f84d4117a21c4c5b", + "37.pdf:md5,004f6f321a744f1ee9dce336ec5ce368", + "38.pdf:md5,f171ff9266ae363381debd592d906bbf", + "39.pdf:md5,d71444767fbcf236fd070ede00827447", + "40.pdf:md5,109d22bdf3013e8827b7c2d5623a03de", + "41.pdf:md5,a25622b8396b3de2fd8fff2c8e5f6023", + "21.pdf:md5,0b84a274a52bdb7fd1447e7e2bc08bcc", + "22.pdf:md5,af3fbb84ede9977371d2ffe0262a3612", + "23.pdf:md5,8d496689c03b1a2162af875b737d7a7e", + "24.pdf:md5,8dd79dcacc29c591cee1973d6084cd73", + "25.pdf:md5,52623acfb30b29c1a1fe9bc9c0e521e1", + "26.pdf:md5,fbf921566dc93d253652b91dc250eaf5", + "27.pdf:md5,2b156fc5a4e6f78c634830127fa4828c", + "28.pdf:md5,f04c99f85baf16b8e80c9d947d1608d8", + "29.pdf:md5,858749bbd6b96adc4edffd660713a306", + "30.pdf:md5,d39b902951aef8f7eb91eb944516f34f", + "22.pdf:md5,3cdc0827f0f78a2ff5c4f0538925185e", + "23.pdf:md5,1fe96c092604ff6be023909956c15d06", + "24.pdf:md5,9b6fc878f8c02b428cce3f1367a495f4", + "25.pdf:md5,09bbc31ccff437b192c8b739fef24393", + "26.pdf:md5,de96c8c1cb891c39f135ba8ba3d236bf", + "27.pdf:md5,0405f1fe10e90e9b9a2139a3318d0f40", + "28.pdf:md5,6bb8509c01a2a48e33dadc91bdceb919", + "29.pdf:md5,3ea1fe39832820a13697de81fa075542", + "30.pdf:md5,0ee3cb1e3abe2fa9341b408379b20b42", + "31.pdf:md5,a6d3cd1226e73837f22d7a3e2d721c47", + "32.pdf:md5,6d7c2c978ed6a5564532c7abe6aef13f", + "21.pdf:md5,63aef7bf79987a7efdf59497ec0102b2", + "22.pdf:md5,48aa1c686dbf7a8c996924d096c248b5", + "23.pdf:md5,19e5184541088896c36677cc745b239a", + "24.pdf:md5,73cf695ba11e9d0c5bb2febd08ba5b1b", + "25.pdf:md5,a5cb9892508e3d47fb28c27461810ac6", + "26.pdf:md5,b89305a32c24fcc420ee60bc25cacd20", + "27.pdf:md5,d6f63e6e060af11d5e2d9ffb8575b7b7", + "28.pdf:md5,ed2309cc69b6ff656b33a41ef4c829bb", + "29.pdf:md5,20dde03d08306f9f5bbbaa94ed1af408", + "30.pdf:md5,f6de2cf0996a1dd1ab57ccffa9b29c77", + "31.pdf:md5,311ec3e48aa744be171d7fd1d51caea9", + "32.pdf:md5,aa20eda82587d0238b287855ecf080b1", + "33.pdf:md5,7a69c7c41100bcc929e3887d06775d4c", + "SRX11780885.codon_usage.pdf:md5,32996f0b0a6e55e01c7b84af674ba76c", + "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", + "SRX11780885.ends_heatmap.pdf:md5,b6d407e043d1327bd89d56e55e10e13e", + "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", + "SRX11780885.frames.pdf:md5,f1e1792e74d3ad9a30bd6fbb7c265666", + "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", + "SRX11780885.frames_stratified.pdf:md5,1bedc6093a8c21755a2810e3f5c027e8", + "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", + "SRX11780885.length_bins_for_psite.pdf:md5,5907ffbc677fdb6bce6e6bddcd163345", + "SRX11780885.length_bins_for_psite.tsv:md5,b6fd5abd7f639276df10698b94d3cc52", + "SRX11780885.length_distribution.pdf:md5,f30fbe51b0b4572fee897adaae435be0", + "SRX11780885.length_distribution.tsv:md5,82bee1b71c13feb716f000d4982ed3cf", + "SRX11780885.metaprofile_psite.pdf:md5,de2f6246f76716a70f4be1e040ab5c03", + "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", + "SRX11780885.psite_region.pdf:md5,252beb0c0106651a078aed66f55c5197", + "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", + "SRX11780886.codon_usage.pdf:md5,a4d9502f8638a03a042f3cdd63f24bdd", + "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", + "SRX11780886.ends_heatmap.pdf:md5,8408e30866ee1b126d0bcb80d8feedac", + "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", + "SRX11780886.frames.pdf:md5,499d3d27b3a6696fe52596a8376673ed", + "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", + "SRX11780886.frames_stratified.pdf:md5,59b1cd202eb90420ac0e602740699e98", + "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", + "SRX11780886.length_bins_for_psite.pdf:md5,41d22a44f7d6a22e77b648c0c7a136c2", + "SRX11780886.length_bins_for_psite.tsv:md5,e226199778c919ad4da4d6ff39379742", + "SRX11780886.length_distribution.pdf:md5,bde4288aba61035072945b0f734ca87d", + "SRX11780886.length_distribution.tsv:md5,b272c92a918a405b2cccba30ff0405e1", + "SRX11780886.metaprofile_psite.pdf:md5,aff1b59dfd81968b2cd069be6f7e3e97", + "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", + "SRX11780886.psite_region.pdf:md5,b37f88b8878f0c99eab31e8b0792eb53", + "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", + "SRX11780887.codon_usage.pdf:md5,068c4b9b63e45d4710a40e4349fa4ee1", + "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", + "SRX11780887.ends_heatmap.pdf:md5,72db436552d24174b8b8a6491498920a", + "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", + "SRX11780887.frames.pdf:md5,9a5760dbe7625fb8ed178aed5b69874c", + "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", + "SRX11780887.frames_stratified.pdf:md5,790392115c6cc2f510689388ff6bb9e1", + "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", + "SRX11780887.length_bins_for_psite.pdf:md5,74bcdd709d56b272101448f3391dc2be", + "SRX11780887.length_bins_for_psite.tsv:md5,545a6874f9f3d82c26f28b04977dfcb8", + "SRX11780887.length_distribution.pdf:md5,8db189e10f63ce755df1a326507873b9", + "SRX11780887.length_distribution.tsv:md5,ce512154c88e9cee2c2a9509f82918e8", + "SRX11780887.metaprofile_psite.pdf:md5,429d137d904b08761ebf34be673b4a53", + "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", + "SRX11780887.psite_region.pdf:md5,8add8c205a0285c6c950c34baad9d718", + "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", + "SRX11780888.codon_usage.pdf:md5,9d0b50911756ca1eecebe0c04e776905", + "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", + "SRX11780888.ends_heatmap.pdf:md5,3b96fffa3873ea6812eabb15d7bf375d", + "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", + "SRX11780888.frames.pdf:md5,3353101b1bd9d043aa30239b0487e992", + "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", + "SRX11780888.frames_stratified.pdf:md5,f94f6cb0cf57a72341e9f40d976a6627", + "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", + "SRX11780888.length_bins_for_psite.pdf:md5,63fb1cff624597eeeb0a8605e7bd4d80", + "SRX11780888.length_bins_for_psite.tsv:md5,f7d9223b388a77dd91c5a41aa89134c7", + "SRX11780888.length_distribution.pdf:md5,218ac34e960a149347b63e218b63cd9a", + "SRX11780888.length_distribution.tsv:md5,3e5ef7ee2e090123cf4c2bc6ea71bb01", + "SRX11780888.metaprofile_psite.pdf:md5,2383ceed219a4f6d3eb11b0bd647d98d", + "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", + "SRX11780888.psite_region.pdf:md5,406e9c04c3fbb160447f2f3eabbceded", + "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", + "SRX11780889.codon_usage.pdf:md5,7fb5c5cd6fd7867d71e6e54771e443d4", + "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", + "SRX11780889.ends_heatmap.pdf:md5,87a2d855899ecdd48903b0a64d1dfa65", + "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", + "SRX11780889.frames.pdf:md5,f39b658e23d29325fd5d0c8bbcf6f842", + "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", + "SRX11780889.frames_stratified.pdf:md5,d041e48dc7e7d06fdedd2b07e7aaf523", + "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", + "SRX11780889.length_bins_for_psite.pdf:md5,a78379a74708d5e041f4a5eab4efc466", + "SRX11780889.length_bins_for_psite.tsv:md5,488b91e071d8bcd3d8933974bd6cf952", + "SRX11780889.length_distribution.pdf:md5,23966f79101d4a81322a227fc9553220", + "SRX11780889.length_distribution.tsv:md5,cc5ae4ad914c8afba7726dccc47f9cd0", + "SRX11780889.metaprofile_psite.pdf:md5,863d8c0cfdad7a42b50983088cd26ffa", + "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", + "SRX11780889.psite_region.pdf:md5,f73967a6824ef6126583e4b4fc3b3406", + "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", + "SRX11780890.codon_usage.pdf:md5,82190aef6afccbfbde0cfb38133c6e3b", + "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", + "SRX11780890.ends_heatmap.pdf:md5,0142f4e8d4e19fba8b640cade3582dd9", + "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", + "SRX11780890.frames.pdf:md5,bff4b8ec7092a29adcf20380a8448cda", + "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", + "SRX11780890.frames_stratified.pdf:md5,443063909c6519d640b6363530ab73ba", + "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", + "SRX11780890.length_bins_for_psite.pdf:md5,5b0b3f7e648c064769ba44cf4f4539ca", + "SRX11780890.length_bins_for_psite.tsv:md5,5bed6cd6fb8f944a6e0e7d9325dce6c3", + "SRX11780890.length_distribution.pdf:md5,f5dab4f7518c0063daad562de8ab5e65", + "SRX11780890.length_distribution.tsv:md5,2ee60618861bde90a7ebcbba7013adfe", + "SRX11780890.metaprofile_psite.pdf:md5,90f7b7c33747f6847d5ed15e61da50c5", + "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", + "SRX11780890.psite_region.pdf:md5,dab5d2c769dde8ff5f46c9c4ff47e381", + "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", + "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", + "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8", + "ribowaltz_metaprofile_stop_mqc.json:md5,9d47939e48ad3a6f47a83dfc3f4cba5d", + "ribowaltz_psite_regions_mqc.tsv:md5,31c7d9a993d3203518ab2a1f66710d55", "treated_vs_control.R_sessionInfo.log:md5,3623a50b4668bfebf502bf7080800996" ] ], @@ -1336,6 +1602,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-12T18:29:17.021616696" + "timestamp": "2026-01-05T13:35:39.30841407" } } \ No newline at end of file From 9805f9fa85bca2ed2dd3830076658b49038527b8 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 5 Jan 2026 14:14:44 +0000 Subject: [PATCH 10/11] fix: Correct ribowaltz PDF path in .nftignore [skip ci] MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The ribowaltz PDFs are published to riboseq_qc/ribowaltz/, not ribowaltz/. This covers both offset_plot/ and ribowaltz_qc/ subdirectories. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 --- tests/.nftignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/.nftignore b/tests/.nftignore index 50d9e70d..20940380 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -47,7 +47,7 @@ quantification/salmon/salmon.merged.transcript_counts.tsv quantification/salmon/salmon.merged.transcript_lengths.tsv quantification/salmon/salmon.merged.transcript_tpm.tsv riboseq_qc/ribotish/*_qual.pdf -ribowaltz/**/*.pdf +riboseq_qc/ribowaltz/**/*.pdf translational_efficiency/anota2seq/*.{buffering,total_mRNA,translated_mRNA,translation}.anota2seq.results.tsv translational_efficiency/*/*.{jpeg,jpg,png,pdf,rds,tsv} translational_efficiency/deltate/*.{translation,translated_mRNA,total_mRNA}.deltate.results.tsv From f1b4db5f40e4d77619a383e674f223fa56c62f4a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 5 Jan 2026 14:17:18 +0000 Subject: [PATCH 11/11] fix: Remove PDF checksums from snapshot files MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit PDF files are non-deterministic and should not be checksummed. The .nftignore already excludes them from future snapshots. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 --- tests/default.nf.test.snap | 131 ----------------------- tests/deltate.nf.test.snap | 131 ----------------------- tests/equalise_read_lengths.nf.test.snap | 131 ----------------------- tests/ribo_removal_bowtie2.nf.test.snap | 131 ----------------------- 4 files changed, 524 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 77eff776..205cca90 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1376,184 +1376,53 @@ "SRX11780889.psite_offset.tsv.gz:md5,b8f5920532f631997588149a2b4e1e48", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", "SRX11780890.psite_offset.tsv.gz:md5,b42eac3c4b9e4c9b0af3be1aeb87907b", - "22.pdf:md5,ff96fe41668ac08c0f3f9fb5c0680f87", - "23.pdf:md5,08529012770c675ce13c0308055a1290", - "24.pdf:md5,b0a3898f7fadec66c3fd76b78a3418bb", - "25.pdf:md5,9df4036da6f993c6b0548a778bfb85b0", - "26.pdf:md5,acec96b469c275a24f922be767042597", - "27.pdf:md5,ad51ebb454a9aa4115a1b8fe6cb118fe", - "28.pdf:md5,3a17dcc005fb8aef99019df993854f3b", - "29.pdf:md5,f863b79366dddd2ad77938d47c70c7da", - "30.pdf:md5,1df1887c2dd3663e96b43861f7e59e33", - "31.pdf:md5,b761107c0da19e583028c543a2bb1dcb", - "32.pdf:md5,6c2010ef5a1bcd396f1039d503d0b839", - "33.pdf:md5,10f308fe63e34f991b400c56ae4c5f22", - "34.pdf:md5,d7d94b0e91b9f21ce301b4a0261f15b1", - "20.pdf:md5,b5fc90c57b7623d34058c1e1f443fb6d", - "21.pdf:md5,7a5a23bb048875f4b03337b8e6e95156", - "22.pdf:md5,f08621259571f7897d5c8fe8b9e70856", - "23.pdf:md5,5eaff57be21bba209e7e5af1a299f129", - "24.pdf:md5,258f5e25f4ad414af6121c64d37cee1b", - "25.pdf:md5,3a78ea64a531fd75c2d83561a828ed48", - "26.pdf:md5,7ee80192588b4e201d7fd5f8a66f41e7", - "27.pdf:md5,390fa464c605fd94f624c2d8d0d503ca", - "28.pdf:md5,42433b185f0a768b17d43b1b2ba931b5", - "29.pdf:md5,fcb5599915f9bb34f2ff62dab5cb14b6", - "30.pdf:md5,1fff444e652733a27461a81f2a67ecb7", - "31.pdf:md5,63c2402bdf282fa02a6880036916c868", - "32.pdf:md5,e7c3f1c201ace5a2a954625a28fd992c", - "33.pdf:md5,b9be9dc8a658af1aefc0674e6abf8216", - "20.pdf:md5,8615aa7e8fa2619c896f187af5050f60", - "21.pdf:md5,a1c0a0b5c2133153b73edc57b2c2624b", - "22.pdf:md5,9a196aa8fccded55354a50071b2d55f7", - "23.pdf:md5,b2dd6467fa97a9b0ba0eafbd6cb3ebb9", - "24.pdf:md5,b7c84bc0a67628130df0880d793606d9", - "25.pdf:md5,0ef497aa187a3ea3267767c3e43cfce2", - "26.pdf:md5,49857b5bf55625ec52f542da5874fbc0", - "27.pdf:md5,8a9130d836f3222512a0b5b2d82ad773", - "28.pdf:md5,5508f6569344f6005469fd6efb7cf7cd", - "29.pdf:md5,9e9674a9e06485a02f9d00e19732e795", - "30.pdf:md5,cf8831ebcc46d40261fd92a90541018b", - "31.pdf:md5,3cfc13f6c217c91f9f7d3df75881e37f", - "32.pdf:md5,dd41f7e9ff808717709a3ebbf19033a7", - "33.pdf:md5,b2098ef729aa410d3775a5ae07631471", - "34.pdf:md5,bcf62211aab1ac6d021c5a5ae522cc77", - "35.pdf:md5,8a6f2cee102059c9c86ef9270f2b5e64", - "36.pdf:md5,666bc0114b4b64997dff268fc708de00", - "37.pdf:md5,24f58ab956049e2baa6008bb16968b70", - "38.pdf:md5,e87ff5178637cc34ce79abe53a3b2af1", - "39.pdf:md5,5e6e9b8b4b6955c54d2d96c25345cf50", - "40.pdf:md5,88cb286404b09c11f7da3860bc042670", - "41.pdf:md5,e091b4424e44fada071ca7821716b682", - "21.pdf:md5,a6000f671bf6c78f62abb1999c834e7b", - "22.pdf:md5,e9f7d62ce8960269725f0394fde34059", - "23.pdf:md5,1af0e699d6c87cfc0af00f5a530e412e", - "24.pdf:md5,11cfd6cea431575856494ed011d6ee7b", - "25.pdf:md5,0fd3060f014a4c8eaec9f16f4bb4bb25", - "26.pdf:md5,5685f442d4f9645bb88ffc64da83cb0a", - "27.pdf:md5,0006c536f3db511a3975dc7499d63b56", - "28.pdf:md5,f09aca89061b38848325e0719ce1c13b", - "29.pdf:md5,45a96021976b700eb7eb4e856a7d12d0", - "30.pdf:md5,77bf2fd9ad91b659351dbc649ca754f7", - "22.pdf:md5,43d91f7522c80bcd923ae23eea0abe59", - "23.pdf:md5,316f9c23fd8188d3980a59d0d2b1fc0f", - "24.pdf:md5,95ddb0d075fdbccdbefb838aeffdc657", - "25.pdf:md5,35e629e635001cdb0375f79af914c1e9", - "26.pdf:md5,140a17db9ea2741843654733f5ffafb0", - "27.pdf:md5,b20894fe508714f5a12c72f21427fc7c", - "28.pdf:md5,0afa10bd2c3ff1b2b3fc0e6cf00935a2", - "29.pdf:md5,28b7883e599ed469e1e9ad5495421512", - "30.pdf:md5,dd8de48398e0db65659e5af83556fceb", - "31.pdf:md5,55149bf34914942d0460cf78cc9379e6", - "32.pdf:md5,337ae56ea06734f728ea8cd24dee60c3", - "21.pdf:md5,4a92f136adea850ec06ad15ef25a659e", - "22.pdf:md5,c71d558df12efe7575a574cbf98b9d71", - "23.pdf:md5,c1dc6a5a53ca5cc53a7c09afc4ff8a54", - "24.pdf:md5,bf83a6b59c0e12ac49d2ab571c476195", - "25.pdf:md5,e2fd74d3d3c33e437faecf35fe856776", - "26.pdf:md5,b0074a92d51cc3140c76fc1e58ce8c45", - "27.pdf:md5,d9442a3ff04b7f8bf526e15160942213", - "28.pdf:md5,a7b6e6d9db00712ea6a468d5644e146e", - "29.pdf:md5,8ae5eda9d5a0e15fb530971a39dbb93f", - "30.pdf:md5,2492123b60a19564bc2c470f9009e2f7", - "31.pdf:md5,1016080a85483299ec5d1c2279c7f512", - "32.pdf:md5,1aeadb318fa9a8a14fad2f44f4872799", - "33.pdf:md5,e5bc3e39838a190a668f0dcc6215f89d", - "SRX11780885.codon_usage.pdf:md5,6d9fe99ee3d61539c30e4c5ef086cc8e", "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", - "SRX11780885.ends_heatmap.pdf:md5,33aed465e5e891df60c844699616a2e1", "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", - "SRX11780885.frames.pdf:md5,4d4bf39daa1eae808993a108ea814111", "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", - "SRX11780885.frames_stratified.pdf:md5,ace0790db1db84aae35f5af90564c6af", "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", - "SRX11780885.length_bins_for_psite.pdf:md5,61cbd584d8d8f5dc2f7c69a4555fa635", "SRX11780885.length_bins_for_psite.tsv:md5,acffe9ec8ae169747ff00edca341fbed", - "SRX11780885.length_distribution.pdf:md5,8b9d49a2a80e5bd28a8d455941c00ddd", "SRX11780885.length_distribution.tsv:md5,3b9a5b39c0921175cc148f83f80cc021", - "SRX11780885.metaprofile_psite.pdf:md5,833e38e10c477455cb530f51451d49f9", "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", - "SRX11780885.psite_region.pdf:md5,bc79d5abb1b0e0526809ef21e3856b4e", "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", - "SRX11780886.codon_usage.pdf:md5,21b402e54fae6c7225ddfb38cbffb8ac", "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", - "SRX11780886.ends_heatmap.pdf:md5,eaa9d8ed5dcdeae2b724a5c3e523df53", "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", - "SRX11780886.frames.pdf:md5,8bdd7d8a4034cccef5c58235e500bb2a", "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", - "SRX11780886.frames_stratified.pdf:md5,5c264e9f5ae4f50fb6b93c5fdf1ab1cc", "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", - "SRX11780886.length_bins_for_psite.pdf:md5,a452e37e7f40bc3e525b7c1c70c4ae89", "SRX11780886.length_bins_for_psite.tsv:md5,37bf7614ba447a9126ade1faed887c54", - "SRX11780886.length_distribution.pdf:md5,9c2b0758fcef7e5efa617578ca79a54f", "SRX11780886.length_distribution.tsv:md5,189af46f3ef51420e9287bc4c5a7a3c7", - "SRX11780886.metaprofile_psite.pdf:md5,113d5f8b45c0f04c64c97d5b11801765", "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", - "SRX11780886.psite_region.pdf:md5,b006d3fda32034c389f130c2eb9adbcd", "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", - "SRX11780887.codon_usage.pdf:md5,778f1c064d09eda48cfc99dc1700255e", "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", - "SRX11780887.ends_heatmap.pdf:md5,a9d7cca78f82f212953f115b37d7ae9e", "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", - "SRX11780887.frames.pdf:md5,e901e50eafe3421fa1a50a917dcf86f9", "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", - "SRX11780887.frames_stratified.pdf:md5,c4222461e5603ce69a64ca7457e0624a", "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", - "SRX11780887.length_bins_for_psite.pdf:md5,9c8afbe0ea660c2423cef34af5615764", "SRX11780887.length_bins_for_psite.tsv:md5,da69569999b3532e0a3b1eb6b3bfb8a4", - "SRX11780887.length_distribution.pdf:md5,c9f6e7361ea0975664a691052f4c104e", "SRX11780887.length_distribution.tsv:md5,06e037385e45e601c59d9d2651811154", - "SRX11780887.metaprofile_psite.pdf:md5,5b4f8c2b0203b31debd6213806897d05", "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", - "SRX11780887.psite_region.pdf:md5,638e649752db0764795476494e1f1f37", "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", - "SRX11780888.codon_usage.pdf:md5,55b12e349d7bac3a0c66b3ceacbb0c3f", "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", - "SRX11780888.ends_heatmap.pdf:md5,abe6bdc3b0ec1c9b6889191a04497a4b", "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", - "SRX11780888.frames.pdf:md5,6998d4e4eb1306ffe72b2b47e9b6e68a", "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", - "SRX11780888.frames_stratified.pdf:md5,065989ee280df06eded6dadf1fadfacd", "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", - "SRX11780888.length_bins_for_psite.pdf:md5,2399009214a300f809cfe370316d7935", "SRX11780888.length_bins_for_psite.tsv:md5,55e239b32b68a229155a572a95594dae", - "SRX11780888.length_distribution.pdf:md5,3993e8b29301363111991a2d3b2c0070", "SRX11780888.length_distribution.tsv:md5,240fbe4c42322625f840478a38f239a7", - "SRX11780888.metaprofile_psite.pdf:md5,12d855ef6f94939eac918ed050e5ba54", "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", - "SRX11780888.psite_region.pdf:md5,64cb644ac90d6f1cf5aa31d96329ede6", "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", - "SRX11780889.codon_usage.pdf:md5,f1365ffa9f2f68cc9362345c57b5f361", "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", - "SRX11780889.ends_heatmap.pdf:md5,25dc463bf4b35cdcbcc9e8e684e82233", "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", - "SRX11780889.frames.pdf:md5,2b8f1e3bc3d791ff1168b30dc3c42923", "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", - "SRX11780889.frames_stratified.pdf:md5,9e0c6978812500ad12fe2e45c5d70a0f", "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", - "SRX11780889.length_bins_for_psite.pdf:md5,b2f282a6f615a477283b036e006e535f", "SRX11780889.length_bins_for_psite.tsv:md5,2a3f0c15f19e5ec9031e0f8b13dc7d0d", - "SRX11780889.length_distribution.pdf:md5,923e699815bb2182b2f5cb6858073962", "SRX11780889.length_distribution.tsv:md5,afd2a7c32de7e20247c36c6068e1f4c5", - "SRX11780889.metaprofile_psite.pdf:md5,c3607af7eb62d3f7e1e5e0b0e22dd2b4", "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", - "SRX11780889.psite_region.pdf:md5,e7588edba46cf8fc0db46ce8ddc643b2", "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", - "SRX11780890.codon_usage.pdf:md5,4bb9478751efcd024d4e5a01c9b0e93b", "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", - "SRX11780890.ends_heatmap.pdf:md5,ee16bbbe9e0bd5c022fca0916655d23b", "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", - "SRX11780890.frames.pdf:md5,be28fe9ce8055223303e71015dd3005e", "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", - "SRX11780890.frames_stratified.pdf:md5,dcbfa207fb28353f8e58dd07e6b25de9", "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", - "SRX11780890.length_bins_for_psite.pdf:md5,2794ef8b1645fded7787591f5b5982b2", "SRX11780890.length_bins_for_psite.tsv:md5,d847ef721250472267b53a80d4e3951e", - "SRX11780890.length_distribution.pdf:md5,9d852a903c936efdde8f069143fc8221", "SRX11780890.length_distribution.tsv:md5,0e59ff544796c53e220547b820b0137d", - "SRX11780890.metaprofile_psite.pdf:md5,7a401300597ec7f8f5f212a8b429e14c", "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", - "SRX11780890.psite_region.pdf:md5,08fbefbf1eba2985ea40eaf060d8b5f8", "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8", diff --git a/tests/deltate.nf.test.snap b/tests/deltate.nf.test.snap index 16198da0..282928b6 100644 --- a/tests/deltate.nf.test.snap +++ b/tests/deltate.nf.test.snap @@ -1420,184 +1420,53 @@ "SRX11780889.psite_offset.tsv.gz:md5,e73bb4cd13df6f92efdbaa7dcf380784", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", "SRX11780890.psite_offset.tsv.gz:md5,4c640cbe8c24465fa1758951af308534", - "22.pdf:md5,e420fbd17e410e63ecb6bc5c148a9027", - "23.pdf:md5,0da0b81ace774fb3adb50ac92bfa2837", - "24.pdf:md5,18db6f0b6b582bdaf3882746c0fb193b", - "25.pdf:md5,59783ebe7c3e6fa7b9932e9e88f81747", - "26.pdf:md5,36c07a6da60cf88393f27b798df24997", - "27.pdf:md5,3ff784471dd7be92bb5f6e3c6220aeac", - "28.pdf:md5,ee8a0f06e132965966c5cddbd331fee7", - "29.pdf:md5,ea3bfe25a85bda489d5c1a094322d16c", - "30.pdf:md5,8aabc0de46f2d6758c1eea728179f24e", - "31.pdf:md5,016ed138663b2cca30b1624269675b5e", - "32.pdf:md5,5ed2b6f441ed625d03189138ecdb6650", - "33.pdf:md5,e51a503da259824f1c9b6ea9a20d7121", - "34.pdf:md5,a3dbc2912f763cf4410597c32e80b2b9", - "20.pdf:md5,1b94766fb1136e56b737323055e05510", - "21.pdf:md5,2401f54c4929caa3ac8b0928ff800622", - "22.pdf:md5,c6f462d7fac004954aeaa3b72a6edb95", - "23.pdf:md5,198e4cbba0ab5f0cb6e1679b3e1090cb", - "24.pdf:md5,6a6f386feb9e40ad15aa3145e72b381c", - "25.pdf:md5,6f7d7264bded8343bd44677ac28d2b09", - "26.pdf:md5,38e0fe4d901ea91f6d69ea26ba47c3bb", - "27.pdf:md5,31f28c21638a2ec5859ac93312402948", - "28.pdf:md5,fbc490183b5c2efb2f7209e12d4e0330", - "29.pdf:md5,7281cba67177732ed09fdae312ce3085", - "30.pdf:md5,bf7b11f43129fa3bfbc7c7c68b09a8c1", - "31.pdf:md5,9229acd16d7bdd2402cfe17d98e3c606", - "32.pdf:md5,c512d5f4b311136247feddf166e65bdb", - "33.pdf:md5,1fc2dd5d779f5840be5df16fea307f34", - "20.pdf:md5,7bc8dfd508164d57ab4ea1876416a9e5", - "21.pdf:md5,ccf2192dc981377cf6a4e0cba3925769", - "22.pdf:md5,0437c16e8f491c6082800fc561d0c151", - "23.pdf:md5,e21271d8e1c7a8c7da166bad315645dd", - "24.pdf:md5,12f8089d806fdef77b693abb6bdd53ce", - "25.pdf:md5,64bcad4c8a44533b452e11c4fc3da704", - "26.pdf:md5,317f8e60fcfdf280e90ed5ef5cdb7fc7", - "27.pdf:md5,1dcf71705a57fcb1774dc75efe40fcd0", - "28.pdf:md5,d12ae70dca790222e39e35ee599f63f9", - "29.pdf:md5,5c8551b35a3906206f187462ba27f35d", - "30.pdf:md5,a265c55756944a99e43fe8bc68c19293", - "31.pdf:md5,2359e72378ec8f5a87302e8fff2d3074", - "32.pdf:md5,7a44b8b00e18b7b8a4c35cf4fb07152d", - "33.pdf:md5,eae4ce4c666359a49c4d9d2f9f049061", - "34.pdf:md5,ab8cce1289e482c2e0b31d50698ed402", - "35.pdf:md5,55d0ec6d620a1d19a1f0fdab0b0cbdb9", - "36.pdf:md5,ddc49d924c3751903cfcb654cf9be1a7", - "37.pdf:md5,d45d8015bcc3d6e4149990b30e480ca2", - "38.pdf:md5,aba3447dd5543363128bf848cca246cf", - "39.pdf:md5,e883a6776bf6a098bc92f1088bc856a3", - "40.pdf:md5,616da789b1c98bbbee6cbcfd86fa551f", - "41.pdf:md5,fdaf259171e0cbc79cd1e16a0dad7e01", - "21.pdf:md5,9b37b12431ec0509889bf2f2a7bdf13c", - "22.pdf:md5,20def5827ecb8f40bba38445d11405bd", - "23.pdf:md5,4f0d4e61730f81f4d6f2ec8fa625d34a", - "24.pdf:md5,7067ff38357082ca26328ee762217635", - "25.pdf:md5,3c7958e8449fc32537d7c3e9e08902a1", - "26.pdf:md5,0b657d71f8a6eb4f0ccf7e88e146008b", - "27.pdf:md5,784c2f458524e8baf2013629326201ae", - "28.pdf:md5,735f72320833b3c1520383baa36053e5", - "29.pdf:md5,71cc5ce4d4408a7a64ab0b819b9661e8", - "30.pdf:md5,020609799b92f9ab766fa6e0a56c1f18", - "22.pdf:md5,f022362fb4dd6a7296cb58056f731b9e", - "23.pdf:md5,916a64de6cc7f523e9e5c0471514055b", - "24.pdf:md5,4aed0321122c9156e436be9a839d2cbd", - "25.pdf:md5,346893619e7b9c0f41acf379aa4c30d3", - "26.pdf:md5,596976611c2b2528add434f643d6ff92", - "27.pdf:md5,5029271934f43e09935f907041de9f8c", - "28.pdf:md5,67fa9cb654d3cb799dc0a3fc98c946b6", - "29.pdf:md5,0df9fb630eebba04dba6328b3ac4f721", - "30.pdf:md5,396d4894a68407a2e61300f9571d37e7", - "31.pdf:md5,d61ee795a30c61f4836d1c318d7b2fbc", - "32.pdf:md5,81662cbf46872ade3711c77ee77b3015", - "21.pdf:md5,fa0ddbff587cfe6734042d4d5acf3620", - "22.pdf:md5,e3322450d3bfbeea1ce3ff5a85243002", - "23.pdf:md5,7f11a7f38bcc98f3838db11a08e23da2", - "24.pdf:md5,c78a1c7455d7b75543349f89b3304b88", - "25.pdf:md5,04aa15f67617b72447240e5123dd634a", - "26.pdf:md5,160bfc510ec70d75b99c357bf778511d", - "27.pdf:md5,06bf380db0046317bb676130338caa0b", - "28.pdf:md5,0b3b50556988c04bdfc086ba4d50cd7f", - "29.pdf:md5,151d2e19b2a31f12257b518b8a8cc3aa", - "30.pdf:md5,6196b9e83299987f5fdd10933457c679", - "31.pdf:md5,2c08a11a51215c01761e0b8e7d4f7173", - "32.pdf:md5,84f0adcb985789280a4b67f150aa876b", - "33.pdf:md5,586ddcaea1558644f0540d4d2efc54f2", - "SRX11780885.codon_usage.pdf:md5,3979d8931a1c22435578e3f68e4b2088", "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", - "SRX11780885.ends_heatmap.pdf:md5,77ac2c50eea98b5ab7b46d1db8dc5a59", "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", - "SRX11780885.frames.pdf:md5,caefae112aea637068cb55fc6999818f", "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", - "SRX11780885.frames_stratified.pdf:md5,83ecb72b9a035398a0320a487c04702b", "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", - "SRX11780885.length_bins_for_psite.pdf:md5,6bb5606c56040540760118ae9e35bf3d", "SRX11780885.length_bins_for_psite.tsv:md5,b6fd5abd7f639276df10698b94d3cc52", - "SRX11780885.length_distribution.pdf:md5,62e40029d295f52f6d5bf4009dfc45e7", "SRX11780885.length_distribution.tsv:md5,82bee1b71c13feb716f000d4982ed3cf", - "SRX11780885.metaprofile_psite.pdf:md5,df461936abff78aec01a388e72f0d274", "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", - "SRX11780885.psite_region.pdf:md5,b676c7d00cf27bec89acaf51281b78ec", "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", - "SRX11780886.codon_usage.pdf:md5,dac0a10dd31a820e59ebd64ee3846df3", "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", - "SRX11780886.ends_heatmap.pdf:md5,eb9079567496a060d8bb68ed675a9bd9", "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", - "SRX11780886.frames.pdf:md5,b36f2eeac22f5897d0872294eb8480d9", "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", - "SRX11780886.frames_stratified.pdf:md5,d44a0c9ee59644a4d4557a255e765445", "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", - "SRX11780886.length_bins_for_psite.pdf:md5,65bca0a0e7857bf70378f73c4f3a5c7a", "SRX11780886.length_bins_for_psite.tsv:md5,e226199778c919ad4da4d6ff39379742", - "SRX11780886.length_distribution.pdf:md5,c0a65db004ed8f4d20bc457c2e69cf65", "SRX11780886.length_distribution.tsv:md5,b272c92a918a405b2cccba30ff0405e1", - "SRX11780886.metaprofile_psite.pdf:md5,f4b3b7fefa1da8b21367645c9567e02b", "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", - "SRX11780886.psite_region.pdf:md5,98a7ec60951edfde99cb551047dd02b5", "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", - "SRX11780887.codon_usage.pdf:md5,896e9179925e55602391d52a93e7b2c4", "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", - "SRX11780887.ends_heatmap.pdf:md5,748edcee82c95e6a499765172331feae", "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", - "SRX11780887.frames.pdf:md5,9dcb834a3ab2cac6889876271c37bf4e", "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", - "SRX11780887.frames_stratified.pdf:md5,6621056d6fc3cc56f3ac0c99ecdaeff6", "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", - "SRX11780887.length_bins_for_psite.pdf:md5,20a09c2daa39f5297cf37ac7cc368579", "SRX11780887.length_bins_for_psite.tsv:md5,545a6874f9f3d82c26f28b04977dfcb8", - "SRX11780887.length_distribution.pdf:md5,d73d72d403245d8c455b2286f1b0b432", "SRX11780887.length_distribution.tsv:md5,ce512154c88e9cee2c2a9509f82918e8", - "SRX11780887.metaprofile_psite.pdf:md5,7710bdc773ced5c0c9d040ed2eae4ee5", "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", - "SRX11780887.psite_region.pdf:md5,232fd20365978dde59655f79ee437822", "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", - "SRX11780888.codon_usage.pdf:md5,4d5cd6fecba80b8643a9a7011e125f79", "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", - "SRX11780888.ends_heatmap.pdf:md5,67138d42d9eaa0b4992298d915a09d94", "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", - "SRX11780888.frames.pdf:md5,19fb4b2cbe0796cc4775a23dd333ea94", "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", - "SRX11780888.frames_stratified.pdf:md5,24e137a5eec062403cab9edbb7634a45", "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", - "SRX11780888.length_bins_for_psite.pdf:md5,bb93faae2665886a4ac73378173160da", "SRX11780888.length_bins_for_psite.tsv:md5,f7d9223b388a77dd91c5a41aa89134c7", - "SRX11780888.length_distribution.pdf:md5,b0e4a1b1bf220eb58f389e35d929de48", "SRX11780888.length_distribution.tsv:md5,3e5ef7ee2e090123cf4c2bc6ea71bb01", - "SRX11780888.metaprofile_psite.pdf:md5,1ce598b1092b7c4a03a3c17a6b89d2ec", "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", - "SRX11780888.psite_region.pdf:md5,b88af13a96a53e5a665a40f222b4324d", "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", - "SRX11780889.codon_usage.pdf:md5,dc60791aa4c9b41ee5fd8bdc3ea4f61f", "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", - "SRX11780889.ends_heatmap.pdf:md5,bdd92550f4b969e70d83f574b6a030de", "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", - "SRX11780889.frames.pdf:md5,eb724ed8ff0b9de5f0a62fd23e437062", "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", - "SRX11780889.frames_stratified.pdf:md5,422d1340ef5347d4fa35b3e81d23e0ca", "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", - "SRX11780889.length_bins_for_psite.pdf:md5,ead7f676e0b94c00f45567f012c433f4", "SRX11780889.length_bins_for_psite.tsv:md5,488b91e071d8bcd3d8933974bd6cf952", - "SRX11780889.length_distribution.pdf:md5,7ee7e138b403f9dc6d1461a7b5b4fd5e", "SRX11780889.length_distribution.tsv:md5,cc5ae4ad914c8afba7726dccc47f9cd0", - "SRX11780889.metaprofile_psite.pdf:md5,3037cd0c68fe42abf633574e22abdd0a", "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", - "SRX11780889.psite_region.pdf:md5,3d245cde8530c5bd8115d97ab6405455", "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", - "SRX11780890.codon_usage.pdf:md5,bb41f0f85f8decf88b98478b4b386983", "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", - "SRX11780890.ends_heatmap.pdf:md5,976114a83fbc33a75e79d78d06656409", "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", - "SRX11780890.frames.pdf:md5,fefb085c84f11618c3e5bea93dbf5855", "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", - "SRX11780890.frames_stratified.pdf:md5,131aa3cbf3ec730d509e8c6b8dd7bff4", "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", - "SRX11780890.length_bins_for_psite.pdf:md5,4b12ae3083276fcbafb0613f46d3c4e8", "SRX11780890.length_bins_for_psite.tsv:md5,5bed6cd6fb8f944a6e0e7d9325dce6c3", - "SRX11780890.length_distribution.pdf:md5,60625ddce69b081a54e00d16a0dbf02a", "SRX11780890.length_distribution.tsv:md5,2ee60618861bde90a7ebcbba7013adfe", - "SRX11780890.metaprofile_psite.pdf:md5,1a1c6d9530a91214267a545024f7d3ca", "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", - "SRX11780890.psite_region.pdf:md5,24a561b95394cbcaa23b3fa42e9d031e", "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8", diff --git a/tests/equalise_read_lengths.nf.test.snap b/tests/equalise_read_lengths.nf.test.snap index 115949e6..9d5f402e 100644 --- a/tests/equalise_read_lengths.nf.test.snap +++ b/tests/equalise_read_lengths.nf.test.snap @@ -1446,184 +1446,53 @@ "SRX11780889.psite_offset.tsv.gz:md5,e73bb4cd13df6f92efdbaa7dcf380784", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", "SRX11780890.psite_offset.tsv.gz:md5,4c640cbe8c24465fa1758951af308534", - "22.pdf:md5,4d77377fc70c5a99ee5031320f763331", - "23.pdf:md5,0a1f5a92e7f837fa0235b200f0b55c4f", - "24.pdf:md5,108eb01fd10a2391d8fc3770910d163c", - "25.pdf:md5,0cd2ade79fbe0e1b4bacc654a6e5bd93", - "26.pdf:md5,c51daa118e895fe1c059ade7c30edf39", - "27.pdf:md5,676d993feb1d74331df622e9f1fb336e", - "28.pdf:md5,875e1a571ffd0e6ae42f94dcb97e2f3e", - "29.pdf:md5,a244170781358fd00205557cd6ec2532", - "30.pdf:md5,f6876b3a0c6c760289407a93eea5020b", - "31.pdf:md5,eea2d82d61fe2a80fddfc956e6b5ef29", - "32.pdf:md5,b14be5294a04638b5811f17702fc6218", - "33.pdf:md5,928f2847fd34a31beb52f40829758d39", - "34.pdf:md5,c010b5b5607a0fd2cbbc7dab2ccc7851", - "20.pdf:md5,aaed45186211589d913dd53260fec69c", - "21.pdf:md5,83b07ef1807fa7db91b97e97cb1826c1", - "22.pdf:md5,7c076bc9427c8cdaedfcb799217cabb4", - "23.pdf:md5,88b08f86fb8719104dbca09e6a31efd3", - "24.pdf:md5,53b13127cf4ad6750beda0dec7b1478e", - "25.pdf:md5,d10e724fafe8f29deaddfa5e22722e11", - "26.pdf:md5,4d506d317c13ce3873a57913bc28e958", - "27.pdf:md5,42d6d32022d0ef9a909aaeb64eca3eca", - "28.pdf:md5,49badfc816cabb1e0603359a9e257582", - "29.pdf:md5,c6bf6156a05e8049d4b7bef83488c9a1", - "30.pdf:md5,ee08554286860ea3828665cef8e18779", - "31.pdf:md5,ee208971d436568c029f761f9c44b84b", - "32.pdf:md5,d2ee13efac1e005f463820dafb40c1cd", - "33.pdf:md5,a7a602a2b9031358b745e5fe4b5c17f2", - "20.pdf:md5,55bddb91f8b05ab15da8c66242eb8b7c", - "21.pdf:md5,7eec37e70d3808e633f8e65a5faaf98d", - "22.pdf:md5,a1da5f20b194b35cd3c18e7476f84d23", - "23.pdf:md5,1f5c38105ae648c7635cf2dafe181cd2", - "24.pdf:md5,2de3e6c24f375f91aef05808c527642f", - "25.pdf:md5,367e7db66dfbb8621854213a5ce90608", - "26.pdf:md5,b87e217faad8f2f3b2a7475ee5e12a4b", - "27.pdf:md5,e302d9b35d8c79c9496d8b3d091a5731", - "28.pdf:md5,e01ef4a07abde53e591b0b17c1768c93", - "29.pdf:md5,5d20a4aa4c1d0b9cc5518eb365dea534", - "30.pdf:md5,f7420fafccfad386690f0a812965a9af", - "31.pdf:md5,e4f7e57833e04d749d0834d68cc57c1b", - "32.pdf:md5,36851da54ccd4930d7d40203cf022f76", - "33.pdf:md5,55a0c5fdd667cecfe7ce688fcbea8325", - "34.pdf:md5,e6a419cd670431342bd24f7632e25f7b", - "35.pdf:md5,be5fb83df663ba29cc28c1b9f4faff96", - "36.pdf:md5,8c280df440539ab2f7d482aa84c5450f", - "37.pdf:md5,4d60a855ae6b0415c15d35bc407a1d7e", - "38.pdf:md5,bfa5f7460c02910b71c77f10e6bd07a8", - "39.pdf:md5,8d66c6887d9bf425f9b991964e28c3ff", - "40.pdf:md5,4dbc7a246a630f9cff2adc8c2c8847e5", - "41.pdf:md5,ba3b057dcb0d1e3c2fd6876da71d1856", - "21.pdf:md5,48d52a1f84d23dde50aa4adde248598d", - "22.pdf:md5,10d987cf7a4b45b82e4d425d4cd518de", - "23.pdf:md5,2d25dfe20e1debe4c6adc337a95376d7", - "24.pdf:md5,6e545bf3da967965dc8fe58f0697c3a8", - "25.pdf:md5,c22e72819436035f0e6683de47efe17d", - "26.pdf:md5,6bf9ffc3234742c670b1bc2e5e5f32b1", - "27.pdf:md5,baefb7e908384846599aca01197b385c", - "28.pdf:md5,0f3cfbe286f4d842e7a0c55280b32825", - "29.pdf:md5,8105fc12c35505429deb0a0da653a2d1", - "30.pdf:md5,4f03245910c8fc6498dd0a9c764b356d", - "22.pdf:md5,a5de6ae8ea4e88373035700387ceb790", - "23.pdf:md5,6bbccb27991fb71744aa408718c4a5e0", - "24.pdf:md5,500c763e78c4471d7d299c26d831157f", - "25.pdf:md5,57c4b3e821771f59fe8f9c6168236a3a", - "26.pdf:md5,2127e1151f0e765e537b594f3b4f0be0", - "27.pdf:md5,e74c800a16f37275f2351cb58fd5535f", - "28.pdf:md5,0105998e3598a7b432ec4dde1c0b4c0d", - "29.pdf:md5,7d807865617191a705a896d8dbc8bd3a", - "30.pdf:md5,cb084d2e3f23fad7f2c3deeca32e95e4", - "31.pdf:md5,9dbab4006b39b3c74d01455b0fb3295f", - "32.pdf:md5,0f6461c6ff9b20841864f5f2bc9092fa", - "21.pdf:md5,a000b48ed1199ed6787afe15a1ee0a88", - "22.pdf:md5,0341d4ab1bde04d742ff89976dca5dce", - "23.pdf:md5,43f5f320f2bb043b78d5c54d305f489c", - "24.pdf:md5,d57b502a396df03709f5195ff7f546de", - "25.pdf:md5,1bc06a5266926eaccbcfdb2f84cd1ef8", - "26.pdf:md5,854ee9abc2efe783d8326128ed85f500", - "27.pdf:md5,23af7d0cf71e61ddd6c61cd33221a679", - "28.pdf:md5,a2b1274dd44b3903bb4f74dd31f8d835", - "29.pdf:md5,01015d7c5adf7e68b9db2b258a1ffe12", - "30.pdf:md5,0e254679b7af776ac7f5adde4dc39d01", - "31.pdf:md5,d51c9c26731930f6bb1b13f272afabdb", - "32.pdf:md5,8505b7f0d502eccfd185b955faf7be58", - "33.pdf:md5,44d4335c375b3792838fa6273cc53676", - "SRX11780885.codon_usage.pdf:md5,1f42417b18e7874eb9eba22b0dbf760d", "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", - "SRX11780885.ends_heatmap.pdf:md5,b219cd10f89cead5846e87e7be0ec896", "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", - "SRX11780885.frames.pdf:md5,df9c8981c10e9ef21165d123d66623b3", "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", - "SRX11780885.frames_stratified.pdf:md5,2476b7e6b72eabe2a5b0b86cdd37d5d5", "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", - "SRX11780885.length_bins_for_psite.pdf:md5,ead05e694d3944242f73245b3d34bdd0", "SRX11780885.length_bins_for_psite.tsv:md5,b6fd5abd7f639276df10698b94d3cc52", - "SRX11780885.length_distribution.pdf:md5,6a9706e257edc17555cab4598b7618e4", "SRX11780885.length_distribution.tsv:md5,82bee1b71c13feb716f000d4982ed3cf", - "SRX11780885.metaprofile_psite.pdf:md5,b7a404bd68a952179606d5ef75c55bec", "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", - "SRX11780885.psite_region.pdf:md5,5914175cb5d9654a740cabfbf5b77e43", "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", - "SRX11780886.codon_usage.pdf:md5,6baa919d0076e209df880671719b1d06", "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", - "SRX11780886.ends_heatmap.pdf:md5,f366b705f84135b9f9904830a2fb5897", "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", - "SRX11780886.frames.pdf:md5,aac90230bd23cdf9c7fa343d3bc96404", "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", - "SRX11780886.frames_stratified.pdf:md5,0926e983558de72f0ecc6cf4fdf4097d", "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", - "SRX11780886.length_bins_for_psite.pdf:md5,c9f4e24cc683e8e66b0310ef5dfb542a", "SRX11780886.length_bins_for_psite.tsv:md5,e226199778c919ad4da4d6ff39379742", - "SRX11780886.length_distribution.pdf:md5,1e5b58fc380bb39aca855ddcd4f8961b", "SRX11780886.length_distribution.tsv:md5,b272c92a918a405b2cccba30ff0405e1", - "SRX11780886.metaprofile_psite.pdf:md5,a7c5af8e75cbc531a9c004a7b915b047", "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", - "SRX11780886.psite_region.pdf:md5,8407ad9b1f38da6189b5d2c4fa354ac3", "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", - "SRX11780887.codon_usage.pdf:md5,e1229b40fa024648fddef9eceb4c8088", "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", - "SRX11780887.ends_heatmap.pdf:md5,3fe0e4375c96792928aae1f01f525406", "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", - "SRX11780887.frames.pdf:md5,c3bf11e1ccc7d05006fdbcc27378ef92", "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", - "SRX11780887.frames_stratified.pdf:md5,72677d4a6793c7cf4769f8ded71602bd", "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", - "SRX11780887.length_bins_for_psite.pdf:md5,5c3a81293bff96761d83963edad16330", "SRX11780887.length_bins_for_psite.tsv:md5,545a6874f9f3d82c26f28b04977dfcb8", - "SRX11780887.length_distribution.pdf:md5,57c47fb920aa893166333da87f2d11c2", "SRX11780887.length_distribution.tsv:md5,ce512154c88e9cee2c2a9509f82918e8", - "SRX11780887.metaprofile_psite.pdf:md5,f3286226dfa230aa23d4acc3293add79", "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", - "SRX11780887.psite_region.pdf:md5,feb1e24772ca172f29f9414d0ef7d617", "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", - "SRX11780888.codon_usage.pdf:md5,3df7a37e3979f41b4e117021a369e47a", "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", - "SRX11780888.ends_heatmap.pdf:md5,83b2490dacae8101706579ea7a0082f0", "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", - "SRX11780888.frames.pdf:md5,f59945fbfea29500063a3351fa807f64", "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", - "SRX11780888.frames_stratified.pdf:md5,c2e3289cb3a39fe4e63a62a0b17ac654", "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", - "SRX11780888.length_bins_for_psite.pdf:md5,241fa1807c496bf0ea7e11a07628363c", "SRX11780888.length_bins_for_psite.tsv:md5,f7d9223b388a77dd91c5a41aa89134c7", - "SRX11780888.length_distribution.pdf:md5,bf45db12cffcf99eb981abb221adc0ca", "SRX11780888.length_distribution.tsv:md5,3e5ef7ee2e090123cf4c2bc6ea71bb01", - "SRX11780888.metaprofile_psite.pdf:md5,b84b2409905f3cb4d5af7f7b011dfb5d", "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", - "SRX11780888.psite_region.pdf:md5,ccc610c32d8fc22b5a2957d11bfd6416", "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", - "SRX11780889.codon_usage.pdf:md5,c9f9e86adb274b15058482310381b1ee", "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", - "SRX11780889.ends_heatmap.pdf:md5,a07d4c583b1eb40bc149c6597592671b", "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", - "SRX11780889.frames.pdf:md5,090c99de1f712453885a5e35676834fe", "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", - "SRX11780889.frames_stratified.pdf:md5,fcbbd9a9b7ad1fef62ffa20f23a57d4e", "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", - "SRX11780889.length_bins_for_psite.pdf:md5,66133c97ebcaf77c37473b4e89a41d05", "SRX11780889.length_bins_for_psite.tsv:md5,488b91e071d8bcd3d8933974bd6cf952", - "SRX11780889.length_distribution.pdf:md5,34c8a52ae0401bf7b06a31820264ed91", "SRX11780889.length_distribution.tsv:md5,cc5ae4ad914c8afba7726dccc47f9cd0", - "SRX11780889.metaprofile_psite.pdf:md5,aa531c475e4d18ab6c9fc84c2926e863", "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", - "SRX11780889.psite_region.pdf:md5,5d65b6d9a1c2878c95893018104d405b", "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", - "SRX11780890.codon_usage.pdf:md5,e5c4e21daee6d4536cc5e7241bf1f4dc", "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", - "SRX11780890.ends_heatmap.pdf:md5,a55d2db23a04d20848cfb5d0384a0478", "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", - "SRX11780890.frames.pdf:md5,8bc7b7355335035bf52692cac9575943", "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", - "SRX11780890.frames_stratified.pdf:md5,ef1909d5da303ea57ae5c1355d8f9207", "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", - "SRX11780890.length_bins_for_psite.pdf:md5,dde92c874794d79570fe244cba1d54f3", "SRX11780890.length_bins_for_psite.tsv:md5,5bed6cd6fb8f944a6e0e7d9325dce6c3", - "SRX11780890.length_distribution.pdf:md5,7263a40fb1b7ef1e0b5614a20f0e7579", "SRX11780890.length_distribution.tsv:md5,2ee60618861bde90a7ebcbba7013adfe", - "SRX11780890.metaprofile_psite.pdf:md5,e4b4442baaaf399c1d29c2c4b871df1e", "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", - "SRX11780890.psite_region.pdf:md5,26ccb8626b4b103b16704f08394fc6c5", "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8", diff --git a/tests/ribo_removal_bowtie2.nf.test.snap b/tests/ribo_removal_bowtie2.nf.test.snap index b0ba5aff..d105e353 100644 --- a/tests/ribo_removal_bowtie2.nf.test.snap +++ b/tests/ribo_removal_bowtie2.nf.test.snap @@ -1412,184 +1412,53 @@ "SRX11780889.psite_offset.tsv.gz:md5,e73bb4cd13df6f92efdbaa7dcf380784", "SRX11780890.best_offset.txt:md5,93ce9d385b8261eea0e90611cb1fa968", "SRX11780890.psite_offset.tsv.gz:md5,4c640cbe8c24465fa1758951af308534", - "22.pdf:md5,9430ce83ba88bfc063e992daae84683a", - "23.pdf:md5,cfdd0bb8e97edb2da7ff95f8571b1182", - "24.pdf:md5,d0872557899188349e07f243dd3f9185", - "25.pdf:md5,c8c03094cfd3fc44c72ca2f0a0f609a1", - "26.pdf:md5,4ff638511158fc6320578c69da6a786e", - "27.pdf:md5,0ba0812644e28dccb9ef8e7f28784719", - "28.pdf:md5,2718e7c79f61411a9f5e35b77cfe7481", - "29.pdf:md5,4c0b358c35e8306ef81e529340e7a6a3", - "30.pdf:md5,41a42232ae2c2fff761c9675b0977b77", - "31.pdf:md5,f6fbb51974b1e0fd52eb7565c9f6ba22", - "32.pdf:md5,4b83c011ba89a5ef6c4779d72fa35443", - "33.pdf:md5,eae09a0f37537bb3b2a12ab8dfe51761", - "34.pdf:md5,64aa815dd2ae738b61a6a751baa82847", - "20.pdf:md5,6ad3d5b7a52606656faa097bc5a94e78", - "21.pdf:md5,d686c13b1b6fbf38ef79e15fb68e8710", - "22.pdf:md5,8d10f224c0f94d4a9c5e33dc9620654f", - "23.pdf:md5,f63ea21962391bf49948670fcc568385", - "24.pdf:md5,4331bd8e1d7430f6baaaadb1d266a374", - "25.pdf:md5,91abeea6ea8c92d16ebb5bf815b96c73", - "26.pdf:md5,9fb35420cb066be5b32b40b7cc598cef", - "27.pdf:md5,9677f167e9ab3825ca243811e02d7415", - "28.pdf:md5,4b544c83d9f990dfb114f6652593d42a", - "29.pdf:md5,b404f950b012e39f5bcb4b7e925b7d96", - "30.pdf:md5,dcd7cfad1dc0144ec59e140199e51722", - "31.pdf:md5,7f6d165553ee660447a7aa6829ec8b44", - "32.pdf:md5,a1c316880a9ed2a6f6c5149a1199b816", - "33.pdf:md5,922bc7e0d1a93cf084e05d5562bb9fb6", - "20.pdf:md5,e7f22dcdb762f266a6c7e04c0b99547e", - "21.pdf:md5,f5200c024e444d346b954ed4eecccebe", - "22.pdf:md5,bb1727b4af2e776ef94b99f5e34ac07c", - "23.pdf:md5,b81663f5e0020cb19b394ea566aa55c9", - "24.pdf:md5,e181e89de74303e7ebb71c82b7c609f8", - "25.pdf:md5,1c900876f445d0bc185bc0b87345132b", - "26.pdf:md5,03c14a2842d2925db112d4c6dfd4fc1a", - "27.pdf:md5,e22f1afd5403fe1c24fb7695cc57d40e", - "28.pdf:md5,e40599ee64d6d2798623f4700277d65e", - "29.pdf:md5,850ace11533bcc418718ec7d864de333", - "30.pdf:md5,33ba00de338cd3c903fa3cf1cac45089", - "31.pdf:md5,39053ccd8e87cecc654324664c3a2d68", - "32.pdf:md5,e355e0868bed871796a494761515fdc5", - "33.pdf:md5,7808e1f34ca19f78b1af08e69033d0b4", - "34.pdf:md5,21d75e2a3692ad72cffd0adc5469c165", - "35.pdf:md5,512771f3d5712c76b615ea279cbecff8", - "36.pdf:md5,815515d31127f482f84d4117a21c4c5b", - "37.pdf:md5,004f6f321a744f1ee9dce336ec5ce368", - "38.pdf:md5,f171ff9266ae363381debd592d906bbf", - "39.pdf:md5,d71444767fbcf236fd070ede00827447", - "40.pdf:md5,109d22bdf3013e8827b7c2d5623a03de", - "41.pdf:md5,a25622b8396b3de2fd8fff2c8e5f6023", - "21.pdf:md5,0b84a274a52bdb7fd1447e7e2bc08bcc", - "22.pdf:md5,af3fbb84ede9977371d2ffe0262a3612", - "23.pdf:md5,8d496689c03b1a2162af875b737d7a7e", - "24.pdf:md5,8dd79dcacc29c591cee1973d6084cd73", - "25.pdf:md5,52623acfb30b29c1a1fe9bc9c0e521e1", - "26.pdf:md5,fbf921566dc93d253652b91dc250eaf5", - "27.pdf:md5,2b156fc5a4e6f78c634830127fa4828c", - "28.pdf:md5,f04c99f85baf16b8e80c9d947d1608d8", - "29.pdf:md5,858749bbd6b96adc4edffd660713a306", - "30.pdf:md5,d39b902951aef8f7eb91eb944516f34f", - "22.pdf:md5,3cdc0827f0f78a2ff5c4f0538925185e", - "23.pdf:md5,1fe96c092604ff6be023909956c15d06", - "24.pdf:md5,9b6fc878f8c02b428cce3f1367a495f4", - "25.pdf:md5,09bbc31ccff437b192c8b739fef24393", - "26.pdf:md5,de96c8c1cb891c39f135ba8ba3d236bf", - "27.pdf:md5,0405f1fe10e90e9b9a2139a3318d0f40", - "28.pdf:md5,6bb8509c01a2a48e33dadc91bdceb919", - "29.pdf:md5,3ea1fe39832820a13697de81fa075542", - "30.pdf:md5,0ee3cb1e3abe2fa9341b408379b20b42", - "31.pdf:md5,a6d3cd1226e73837f22d7a3e2d721c47", - "32.pdf:md5,6d7c2c978ed6a5564532c7abe6aef13f", - "21.pdf:md5,63aef7bf79987a7efdf59497ec0102b2", - "22.pdf:md5,48aa1c686dbf7a8c996924d096c248b5", - "23.pdf:md5,19e5184541088896c36677cc745b239a", - "24.pdf:md5,73cf695ba11e9d0c5bb2febd08ba5b1b", - "25.pdf:md5,a5cb9892508e3d47fb28c27461810ac6", - "26.pdf:md5,b89305a32c24fcc420ee60bc25cacd20", - "27.pdf:md5,d6f63e6e060af11d5e2d9ffb8575b7b7", - "28.pdf:md5,ed2309cc69b6ff656b33a41ef4c829bb", - "29.pdf:md5,20dde03d08306f9f5bbbaa94ed1af408", - "30.pdf:md5,f6de2cf0996a1dd1ab57ccffa9b29c77", - "31.pdf:md5,311ec3e48aa744be171d7fd1d51caea9", - "32.pdf:md5,aa20eda82587d0238b287855ecf080b1", - "33.pdf:md5,7a69c7c41100bcc929e3887d06775d4c", - "SRX11780885.codon_usage.pdf:md5,32996f0b0a6e55e01c7b84af674ba76c", "SRX11780885.codon_usage.tsv:md5,bdeaa234ddaf8182a2c9b3bbbca5d9d5", - "SRX11780885.ends_heatmap.pdf:md5,b6d407e043d1327bd89d56e55e10e13e", "SRX11780885.ends_heatmap.tsv:md5,a0990c2e0384dd4e368985f468ef0b91", - "SRX11780885.frames.pdf:md5,f1e1792e74d3ad9a30bd6fbb7c265666", "SRX11780885.frames.tsv:md5,c7acd755b371c07910155e926a7598d9", - "SRX11780885.frames_stratified.pdf:md5,1bedc6093a8c21755a2810e3f5c027e8", "SRX11780885.frames_stratified.tsv:md5,109234eb9274f0f97174a1d5780689f6", - "SRX11780885.length_bins_for_psite.pdf:md5,5907ffbc677fdb6bce6e6bddcd163345", "SRX11780885.length_bins_for_psite.tsv:md5,b6fd5abd7f639276df10698b94d3cc52", - "SRX11780885.length_distribution.pdf:md5,f30fbe51b0b4572fee897adaae435be0", "SRX11780885.length_distribution.tsv:md5,82bee1b71c13feb716f000d4982ed3cf", - "SRX11780885.metaprofile_psite.pdf:md5,de2f6246f76716a70f4be1e040ab5c03", "SRX11780885.metaprofile_psite.tsv:md5,7206697e22ab11b7d1e52525ff9aca1b", - "SRX11780885.psite_region.pdf:md5,252beb0c0106651a078aed66f55c5197", "SRX11780885.psite_region.tsv:md5,5c1a76d43e8fad87d2568a25c86c309d", - "SRX11780886.codon_usage.pdf:md5,a4d9502f8638a03a042f3cdd63f24bdd", "SRX11780886.codon_usage.tsv:md5,4265f4e4a4c3ee8f562271b2933668ca", - "SRX11780886.ends_heatmap.pdf:md5,8408e30866ee1b126d0bcb80d8feedac", "SRX11780886.ends_heatmap.tsv:md5,42e62135b174db6fbf2d574ef1412b4f", - "SRX11780886.frames.pdf:md5,499d3d27b3a6696fe52596a8376673ed", "SRX11780886.frames.tsv:md5,862ba80df88dddeccf065729b20fb795", - "SRX11780886.frames_stratified.pdf:md5,59b1cd202eb90420ac0e602740699e98", "SRX11780886.frames_stratified.tsv:md5,d013ebeadc2f336db10cf8fd3071a704", - "SRX11780886.length_bins_for_psite.pdf:md5,41d22a44f7d6a22e77b648c0c7a136c2", "SRX11780886.length_bins_for_psite.tsv:md5,e226199778c919ad4da4d6ff39379742", - "SRX11780886.length_distribution.pdf:md5,bde4288aba61035072945b0f734ca87d", "SRX11780886.length_distribution.tsv:md5,b272c92a918a405b2cccba30ff0405e1", - "SRX11780886.metaprofile_psite.pdf:md5,aff1b59dfd81968b2cd069be6f7e3e97", "SRX11780886.metaprofile_psite.tsv:md5,5d4d5448eb83d922ce14ff4bed4a53a4", - "SRX11780886.psite_region.pdf:md5,b37f88b8878f0c99eab31e8b0792eb53", "SRX11780886.psite_region.tsv:md5,82e738b90d76a99692763f5c6e22e37d", - "SRX11780887.codon_usage.pdf:md5,068c4b9b63e45d4710a40e4349fa4ee1", "SRX11780887.codon_usage.tsv:md5,d7b51ef2d0da1149197bf0b17ab5b911", - "SRX11780887.ends_heatmap.pdf:md5,72db436552d24174b8b8a6491498920a", "SRX11780887.ends_heatmap.tsv:md5,ab85302314a7f76186b667389c984304", - "SRX11780887.frames.pdf:md5,9a5760dbe7625fb8ed178aed5b69874c", "SRX11780887.frames.tsv:md5,add6f8a37e17e97a6278f938a26d002b", - "SRX11780887.frames_stratified.pdf:md5,790392115c6cc2f510689388ff6bb9e1", "SRX11780887.frames_stratified.tsv:md5,d945bb2adba33ad506a6437c1051b754", - "SRX11780887.length_bins_for_psite.pdf:md5,74bcdd709d56b272101448f3391dc2be", "SRX11780887.length_bins_for_psite.tsv:md5,545a6874f9f3d82c26f28b04977dfcb8", - "SRX11780887.length_distribution.pdf:md5,8db189e10f63ce755df1a326507873b9", "SRX11780887.length_distribution.tsv:md5,ce512154c88e9cee2c2a9509f82918e8", - "SRX11780887.metaprofile_psite.pdf:md5,429d137d904b08761ebf34be673b4a53", "SRX11780887.metaprofile_psite.tsv:md5,d56b0ddbaa10e3c6c255744c7777aae1", - "SRX11780887.psite_region.pdf:md5,8add8c205a0285c6c950c34baad9d718", "SRX11780887.psite_region.tsv:md5,b0ae533d791cb6fce99f907e413078c0", - "SRX11780888.codon_usage.pdf:md5,9d0b50911756ca1eecebe0c04e776905", "SRX11780888.codon_usage.tsv:md5,b4296e8cb4903720e17770ac7591831c", - "SRX11780888.ends_heatmap.pdf:md5,3b96fffa3873ea6812eabb15d7bf375d", "SRX11780888.ends_heatmap.tsv:md5,5347d7a864774bf25defadf276ac4d6b", - "SRX11780888.frames.pdf:md5,3353101b1bd9d043aa30239b0487e992", "SRX11780888.frames.tsv:md5,863d1a0cd5f1838b23d0ce83f5c461a5", - "SRX11780888.frames_stratified.pdf:md5,f94f6cb0cf57a72341e9f40d976a6627", "SRX11780888.frames_stratified.tsv:md5,621088df9ed88acd80bb8a22f9910582", - "SRX11780888.length_bins_for_psite.pdf:md5,63fb1cff624597eeeb0a8605e7bd4d80", "SRX11780888.length_bins_for_psite.tsv:md5,f7d9223b388a77dd91c5a41aa89134c7", - "SRX11780888.length_distribution.pdf:md5,218ac34e960a149347b63e218b63cd9a", "SRX11780888.length_distribution.tsv:md5,3e5ef7ee2e090123cf4c2bc6ea71bb01", - "SRX11780888.metaprofile_psite.pdf:md5,2383ceed219a4f6d3eb11b0bd647d98d", "SRX11780888.metaprofile_psite.tsv:md5,f877bee6c165119819c7acea9927dfb5", - "SRX11780888.psite_region.pdf:md5,406e9c04c3fbb160447f2f3eabbceded", "SRX11780888.psite_region.tsv:md5,efe0278d01f27eb46478f3e5d7a206c3", - "SRX11780889.codon_usage.pdf:md5,7fb5c5cd6fd7867d71e6e54771e443d4", "SRX11780889.codon_usage.tsv:md5,2bd686f79ded8b794437c03fef543cce", - "SRX11780889.ends_heatmap.pdf:md5,87a2d855899ecdd48903b0a64d1dfa65", "SRX11780889.ends_heatmap.tsv:md5,3aa3dce1435cedee841da9b3f349379a", - "SRX11780889.frames.pdf:md5,f39b658e23d29325fd5d0c8bbcf6f842", "SRX11780889.frames.tsv:md5,3861dd9618ced7c9d768169c4fa763b2", - "SRX11780889.frames_stratified.pdf:md5,d041e48dc7e7d06fdedd2b07e7aaf523", "SRX11780889.frames_stratified.tsv:md5,0bea7b12bc24a52e6586493881a3186a", - "SRX11780889.length_bins_for_psite.pdf:md5,a78379a74708d5e041f4a5eab4efc466", "SRX11780889.length_bins_for_psite.tsv:md5,488b91e071d8bcd3d8933974bd6cf952", - "SRX11780889.length_distribution.pdf:md5,23966f79101d4a81322a227fc9553220", "SRX11780889.length_distribution.tsv:md5,cc5ae4ad914c8afba7726dccc47f9cd0", - "SRX11780889.metaprofile_psite.pdf:md5,863d8c0cfdad7a42b50983088cd26ffa", "SRX11780889.metaprofile_psite.tsv:md5,6e5393d4eaf88588acf3ea60aaaac1f4", - "SRX11780889.psite_region.pdf:md5,f73967a6824ef6126583e4b4fc3b3406", "SRX11780889.psite_region.tsv:md5,0757fb231a5a9b7422229616f9de34cb", - "SRX11780890.codon_usage.pdf:md5,82190aef6afccbfbde0cfb38133c6e3b", "SRX11780890.codon_usage.tsv:md5,f0fbe20421aed23650aac435c1d53744", - "SRX11780890.ends_heatmap.pdf:md5,0142f4e8d4e19fba8b640cade3582dd9", "SRX11780890.ends_heatmap.tsv:md5,c7865d3c87af20f18fd2642efbd23de7", - "SRX11780890.frames.pdf:md5,bff4b8ec7092a29adcf20380a8448cda", "SRX11780890.frames.tsv:md5,aba5248611258d7ba31572a39bdc4511", - "SRX11780890.frames_stratified.pdf:md5,443063909c6519d640b6363530ab73ba", "SRX11780890.frames_stratified.tsv:md5,902b4a9bc8c719eb76dbab8ccffe72cd", - "SRX11780890.length_bins_for_psite.pdf:md5,5b0b3f7e648c064769ba44cf4f4539ca", "SRX11780890.length_bins_for_psite.tsv:md5,5bed6cd6fb8f944a6e0e7d9325dce6c3", - "SRX11780890.length_distribution.pdf:md5,f5dab4f7518c0063daad562de8ab5e65", "SRX11780890.length_distribution.tsv:md5,2ee60618861bde90a7ebcbba7013adfe", - "SRX11780890.metaprofile_psite.pdf:md5,90f7b7c33747f6847d5ed15e61da50c5", "SRX11780890.metaprofile_psite.tsv:md5,1312f576256da60efdfb532df7e7b1a9", - "SRX11780890.psite_region.pdf:md5,dab5d2c769dde8ff5f46c9c4ff47e381", "SRX11780890.psite_region.tsv:md5,1a64e419a09e5c4bc72f078207c591e0", "ribowaltz_frames_mqc.tsv:md5,e4b58fd75ae8d18e222dab58c63e1904", "ribowaltz_metaprofile_start_mqc.json:md5,4d0944380daaccce45aa80cb99200fe8",