diff --git a/CHANGELOG.md b/CHANGELOG.md index 2e7fb21a..82b06d70 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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)) - [#138](https://github.com/nf-core/riboseq/pull/138) - Add MultiQC configuration for BBSplit, Bowtie2 rRNA removal, UMItools, and UMIcollapse ([@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` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 57c47d54..7b5f2214 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,6 +1,57 @@ 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 + # 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 + 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: @@ -47,21 +98,9 @@ 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" - module_order: - fastqc: + anchor: "fastqc_raw" name: "FastQC (raw)" info: "This section of the report shows FastQC results before adapter trimming." path_filters: @@ -79,6 +118,7 @@ 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: @@ -90,6 +130,7 @@ module_order: info: "Bowtie2 alignment statistics for rRNA removal. Reads were aligned against an rRNA reference to filter out ribosomal RNA contamination." - star - samtools + - ribowaltz - umitools - umicollapse - ribotish diff --git a/bin/ribowaltz_to_mqc.py b/bin/ribowaltz_to_mqc.py new file mode 100755 index 00000000..3668b32f --- /dev/null +++ b/bin/ribowaltz_to_mqc.py @@ -0,0 +1,171 @@ +#!/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 + +# Common constants +PARENT_ID = "ribowaltz" +PARENT_NAME = "riboWaltz" +PARENT_DESC = 'Quality control metrics from riboWaltz for assessing Ribo-seq data quality.' + +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"} + + +def read_tsv_files(files): + """Yield rows from multiple TSV files.""" + for filepath in files: + with open(filepath, 'r') as f: + yield from csv.DictReader(f, delimiter='\t') + + +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(f"# id: '{plot_id}_plot'") + print(f"# title: '{PARENT_NAME}: {section_name}'") + print(f"# ylab: '{ylab}'") + print("# cpswitch: false") + + +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] + print(f"RNA-seq reference\t" + "\t".join(values)) + 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.""" + data = defaultdict(lambda: defaultdict(dict)) + frames = ["Frame 0", "Frame 1", "Frame 2"] + 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"} + + 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()) + + 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." + ) + + if samples: + print("# sample_groups:") + for region in region_keys: + label = region_labels[region] + print(f'# "{label}":') + for sample in samples: + print(f'# - ["{sample}_{label}", "{sample}"]') + + print("Sample\t" + "\t".join(frames)) + for sample in samples: + for region in region_keys: + label = region_labels[region] + values = [str(round(data[sample][region].get(f, 0), 1)) for f in frames] + print(f"{sample}_{label}\t" + "\t".join(values)) + + +def transform_metaprofile(files, region_filter): + """Transform metaprofile_psite.tsv files to MultiQC linegraph JSON format.""" + data = defaultdict(list) + target_region = f"Distance from {region_filter} (nt)" + + 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 sample in data: + 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": 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"{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)) + + +if __name__ == "__main__": + if len(sys.argv) < 3: + print(__doc__, file=sys.stderr) + sys.exit(1) + + 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) + 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..3e25a172 --- /dev/null +++ b/subworkflows/local/ribowaltz_qc/main.nf @@ -0,0 +1,64 @@ +// +// 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 + // + RIBOWALTZ.out.ribowaltz_qc_data + .map { meta, files -> files } + .flatten() + .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_qc.psite_region.collect(), + ch_ribowaltz_qc.frames.collect(), + ch_ribowaltz_qc.metaprofile.collect() + ) + + 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/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 diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8b8a507f..205cca90 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", + 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"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", - 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"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", + 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+ "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", @@ 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"ribowaltz_metaprofile_stop_mqc.json:md5,9d47939e48ad3a6f47a83dfc3f4cba5d", + "ribowaltz_psite_regions_mqc.tsv:md5,31c7d9a993d3203518ab2a1f66710d55", "treated_vs_control.R_sessionInfo.log:md5,9388c2a7f77dfde471cd9b67687070e4" ] ], @@ -1344,6 +1479,6 @@ "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..9d5f402e 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", - 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"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", + 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"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", + 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"treated_vs_control.R_sessionInfo.log:md5,3623a50b4668bfebf502bf7080800996" ] ], @@ -1370,6 +1505,6 @@ "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..d105e353 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", + 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"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", 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"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", - 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"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", + 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at end of file 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) } //