diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2e7fb21a..03b3a2cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#125](https://github.com/nf-core/riboseq/pull/125) - Add rRNA removal tool selection with support for SortMeRNA (default), Bowtie2, and RiboDetector ([@pinin4fjords](https://github.com/pinin4fjords))
- [#128](https://github.com/nf-core/riboseq/pull/128) - Add DESeq2-based deltaTE analysis as an alternative to anota2seq for translational efficiency analysis ([@pinin4fjords](https://github.com/pinin4fjords))
- [#131](https://github.com/nf-core/riboseq/pull/131) - Add ribotish quality output routing to MultiQC ([@pinin4fjords](https://github.com/pinin4fjords))
+- [#134](https://github.com/nf-core/riboseq/pull/134) - Add P-site identification using plastid ([@suhrig](https://github.com/suhrig))
- [#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))
@@ -23,22 +24,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Parameters`
-| Old parameter | New parameter |
-| ------------- | ----------------------------------- |
-| | `--ribo_removal_tool` |
-| | `--translational_efficiency_method` |
-| | `--extra_deltate_args` |
-| | `--te_lfc_threshold` |
-| | `--rna_lfc_threshold` |
-| | `--ribo_lfc_threshold` |
-| | `--equalise_read_lengths` |
-| | `--equalise_read_lengths_target` |
+| Old parameter | New parameter |
+| ------------- | ---------------------------------------- |
+| | `--ribo_removal_tool` |
+| | `--translational_efficiency_method` |
+| | `--extra_deltate_args` |
+| | `--te_lfc_threshold` |
+| | `--rna_lfc_threshold` |
+| | `--ribo_lfc_threshold` |
+| | `--equalise_read_lengths` |
+| | `--equalise_read_lengths_target` |
+| | `--skip_plastid` |
+| | `--plastid_min_length` |
+| | `--plastid_max_length` |
+| | `--plastid_default_psite_offset` |
+| | `--extra_plastid_metagene_generate_args` |
+| | `--extra_plastid_psite_args` |
+| | `--extra_plastid_make_wiggle_args` |
### `Dependencies`
| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `MultiQC` | 1.32 | 1.33 |
+| `plastid` | | 0.6.1 |
## v1.2.0 - 2025-12-03
diff --git a/README.md b/README.md
index 5ae566f0..89d258fe 100644
--- a/README.md
+++ b/README.md
@@ -41,7 +41,7 @@ Differences occur in the downstream analysis steps. Currently these specialist s
1. Check reads distribution around annotated protein coding regions on user provided transcripts, show frame bias and estimate P-site offset for different group of reads ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))
2. (default, optional) Predict translated open reading frames and/ or translation initiation sites _de novo_ from alignment data ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))
3. (default, optional) Derive candidate ORFs from reference data and detect translated ORFs from that list ([`Ribotricer`](https://github.com/smithlabcode/ribotricer))
-4. (default, optional) Derive P-sites and QC from transcriptome alignments ([`riboWaltz`](https://github.com/LabTranslationalArchitectomics/riboWaltz))
+4. (default, optional) Derive P-sites and QC from transcriptome alignments ([`riboWaltz`](https://github.com/LabTranslationalArchitectomics/riboWaltz), [`plastid`](https://plastid.readthedocs.io/en/latest/index.html))
5. (optional) Use a translational efficiency approach to study the dynamics of transcription and translation, with [anota2seq](https://bioconductor.org/packages/release/bioc/html/anota2seq.html). **requires matched RNA-seq and Ribo-seq data**
## Usage
diff --git a/conf/modules.config b/conf/modules.config
index a4716a76..489ccbab 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -973,6 +973,53 @@ if (!params.skip_ribowaltz) {
process {
withName: 'RIBOWALTZ' {
ext.args = { params.extra_ribowaltz_args ?: '' }
+ publishDir = [
+ path: { "${params.outdir}/psites/ribowaltz" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ }
+ }
+}
+
+if (!params.skip_plastid) {
+ process {
+ withName: 'PLASTID_METAGENE_GENERATE' {
+ ext.args = { [
+ params.extra_plastid_metagene_generate_args ?: '',
+ '--landmark cds_start'
+ ].join(' ').trim() }
+ publishDir = [
+ path: { "${params.outdir}/psites/plastid/metagene" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ }
+ withName: 'PLASTID_PSITE' {
+ ext.args = { [
+ params.extra_plastid_psite_args ?: '',
+ params.plastid_min_length ? "--min_length ${params.plastid_min_length}" : '',
+ params.plastid_max_length ? "--max_length ${params.plastid_max_length}" : '',
+ params.plastid_default_psite_offset ? "--default ${params.plastid_default_psite_offset}" : '',
+ '--require_upstream',
+ ].join(' ').trim() }
+ publishDir = [
+ path: { "${params.outdir}/psites/plastid/offsets" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ }
+ withName: 'PLASTID_MAKE_WIGGLE' {
+ ext.args = { [
+ params.extra_plastid_make_wiggle_args ?: '',
+ params.plastid_min_length ? "--min_length ${params.plastid_min_length}" : '',
+ '--output_format bedgraph'
+ ].join(' ').trim() }
+ publishDir = [
+ path: { "${params.outdir}/psites/plastid/tracks" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
}
}
}
diff --git a/docs/output.md b/docs/output.md
index 26d79994..74cb56c0 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -36,6 +36,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [Ribotricer detect-orfs](#ribotricer-detect-orfs)
- [P-site identification](#p-site-identification)
- [riboWaltz](#ribowaltz)
+ - [plastid](#plastid)
- [Quantification](#quantification)
- [Translational efficiency](#translational-efficiency)
- [MultiQC](#multiqc)
@@ -372,6 +373,19 @@ P-sites are identified by passing transcriptome-level alignment BAM files to rib
+P-sites are identified by passing genome-level alignment BAM files to plastid, producing the following outputs:
+
+
+Output files
+
+- `plastid/`
+ - `*.filtered_rois.bed` and `*.filtered_rois.txt`: Position of CDS start for each gene in BED or TXT format; used for metagene analysis
+ - `*_metagene_profiles.txt`: Matrix containing the distances of the 5' read ends to the CDS start position for each read length
+ - `*_p_offsets.png`: Graphical illustrations of the metagene profiles
+ - `*_p_offsets.txt`: Selected Optimal p-site offset for each read length
+
+
+
## Quantification
Quantification is done by passing transcriptome-level alignment BAM files to Salmon, producing the following outputs:
diff --git a/docs/usage.md b/docs/usage.md
index a46da4fb..c691d703 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -298,6 +298,8 @@ The pipeline will by default run the [Ribo-TISH](https://github.com/zhpn1024/rib
The pipeline will by default run [riboWaltz](https://github.com/LabTranslationalArchitectomics/riboWaltz) for P-site identification and diagnostics, unless disabled with `--skip_ribowaltz`. Additional arguments can be supplied via `--extra_ribowaltz_args` parameters. An example is: `--extra_ribowaltz_args "--length_range 27:31 --periodicity_threshold 40 --extremity 5end --start_nts 45 --stop_nts 24"`. If not provided, defaults used in the [nf-core module](https://github.com/nf-core/modules/blob/master/modules/nf-core/ribowaltz/templates/ribowaltz.r) are used.
+In addition, the pipeline runs [plastid](https://plastid.readthedocs.io/en/latest/index.html) to identify P-sites and create bedGraph tracks, unless disabled with `--skip_plastid`.
+
## Translational efficiency
If you have paired RNA-seq and Riboseq samples, you can use this workflow to initiate a translational efficiency analysis.
diff --git a/modules.json b/modules.json
index 89ea4fd3..c63f0dbf 100644
--- a/modules.json
+++ b/modules.json
@@ -95,6 +95,21 @@
"git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
"installed_by": ["modules"]
},
+ "plastid/make_wiggle": {
+ "branch": "master",
+ "git_sha": "8d66ebdfc2e09f449c03dcb3a08a9ee13f0412d3",
+ "installed_by": ["modules"]
+ },
+ "plastid/metagene_generate": {
+ "branch": "master",
+ "git_sha": "8d66ebdfc2e09f449c03dcb3a08a9ee13f0412d3",
+ "installed_by": ["modules"]
+ },
+ "plastid/psite": {
+ "branch": "master",
+ "git_sha": "8d66ebdfc2e09f449c03dcb3a08a9ee13f0412d3",
+ "installed_by": ["modules"]
+ },
"ribodetector": {
"branch": "master",
"git_sha": "61ce58ac3e4e4627d9c1cdc958ee6bfa742a0a75",
diff --git a/modules/nf-core/plastid/make_wiggle/environment.yml b/modules/nf-core/plastid/make_wiggle/environment.yml
new file mode 100644
index 00000000..86ff4ca2
--- /dev/null
+++ b/modules/nf-core/plastid/make_wiggle/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - plastid=0.6.1
diff --git a/modules/nf-core/plastid/make_wiggle/main.nf b/modules/nf-core/plastid/make_wiggle/main.nf
new file mode 100644
index 00000000..78adce16
--- /dev/null
+++ b/modules/nf-core/plastid/make_wiggle/main.nf
@@ -0,0 +1,68 @@
+process PLASTID_MAKE_WIGGLE {
+ tag "$meta.id"
+ label "process_single"
+
+ // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+ conda "${moduleDir}/environment.yml"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/plastid:0.6.1--py39had3e4b6_2':
+ 'biocontainers/plastid:0.6.1--py39had3e4b6_2' }"
+
+ input:
+ tuple val(meta), path(bam), path(bam_index), path(p_offsets)
+ val(mapping_rule)
+
+ output:
+ tuple val(meta), path("*.{wig,bedgraph}"), emit: tracks
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ if (mapping_rule == 'fiveprime_variable' && !p_offsets) {
+ error "p_offsets file is required when using mapping_rule 'fiveprime_variable'"
+ }
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def args = task.ext.args ?: ""
+ def offset_arg = mapping_rule == 'fiveprime_variable' ? "--offset $p_offsets" : ""
+ def extension = args.contains('--output_format bedgraph') ? "bedgraph" : "wig"
+ def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+ """
+ make_wiggle \\
+ --count_files "$bam" \\
+ $offset_arg \\
+ --${mapping_rule} \\
+ -o "$prefix" \\
+ $args
+
+ if [ "$extension" = "bedgraph" ]; then
+ for FILE in *.wig; do
+ mv "\$FILE" "\${FILE%.wig}.bedgraph"
+ done
+ fi
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ plastid: $VERSION
+ END_VERSIONS
+ """
+
+ stub:
+ if (mapping_rule == 'fiveprime_variable' && !p_offsets) {
+ error "p_offsets file is required when using mapping_rule 'fiveprime_variable'"
+ }
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def args = task.ext.args ?: ""
+ def extension = args.contains('--output_format bedgraph') ? "bedgraph" : "wig"
+ def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+ """
+ touch ${prefix}_fw.${extension}
+ touch ${prefix}_rc.${extension}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ plastid: $VERSION
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/plastid/make_wiggle/meta.yml b/modules/nf-core/plastid/make_wiggle/meta.yml
new file mode 100644
index 00000000..a78feea6
--- /dev/null
+++ b/modules/nf-core/plastid/make_wiggle/meta.yml
@@ -0,0 +1,77 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "plastid_make_wiggle"
+description: Create wiggle or bedGraph files from alignment files after applying
+ a read mapping rule (e.g. to map ribosome-protected footprints at their
+ P-sites), for visualization in a genome browser
+keywords:
+ - genomics
+ - riboseq
+ - psite
+ - wiggle
+ - bedgraph
+tools:
+ - "plastid":
+ description: "Nucleotide-resolution analysis of next-generation sequencing and
+ genomics data"
+ homepage: "https://github.com/joshuagryphon/plastid"
+ documentation: "https://plastid.readthedocs.io/en/latest/"
+ tool_dev_url: "https://github.com/joshuagryphon/plastid"
+ doi: "10.1186/s12864-016-3278-x"
+ licence: ["BSD-3-clause"]
+ identifier: biotools:plastid
+
+input:
+ - - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - bam:
+ type: file
+ description: Genome BAM file
+ pattern: "*.bam"
+ ontologies:
+ - edam: http://edamontology.org/format_2572 # BAM
+ - bam_index:
+ type: file
+ description: Genome BAM index file
+ pattern: "*.bai"
+ ontologies:
+ - edam: http://edamontology.org/format_3327 # BAI
+ - p_offsets:
+ type: file
+ description: |
+ Selected p-site offset for each read length (output from plastid_psite).
+ Required when mapping_rule is 'fiveprime_variable', otherwise pass empty list [].
+ pattern: "*_p_offsets.txt"
+ ontologies: []
+ - mapping_rule:
+ type: string
+ description: |
+ Read mapping rule. Use 'fiveprime_variable' with p_offsets file to map reads to P-sites.
+ enum: ["fiveprime", "threeprime", "center", "fiveprime_variable"]
+output:
+ tracks:
+ - - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - "*.{wig,bedgraph}":
+ type: file
+ description: wig/bedgraph tracks for forward and reverse strands
+ pattern: "*.{wig,bedgraph}"
+ ontologies:
+ - edam: http://edamontology.org/format_3005 # wig
+ - edam: http://edamontology.org/format_3583 # bedgraph
+ versions:
+ - versions.yml:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ ontologies:
+ - edam: http://edamontology.org/format_3750 # YAML
+authors:
+ - "@suhrig"
+maintainers:
+ - "@suhrig"
diff --git a/modules/nf-core/plastid/make_wiggle/tests/main.nf.test b/modules/nf-core/plastid/make_wiggle/tests/main.nf.test
new file mode 100644
index 00000000..8aa562eb
--- /dev/null
+++ b/modules/nf-core/plastid/make_wiggle/tests/main.nf.test
@@ -0,0 +1,65 @@
+// nf-core modules test plastid
+nextflow_process {
+
+ name "Test Process PLASTID_MAKE_WIGGLE"
+ script "../main.nf"
+ process "PLASTID_MAKE_WIGGLE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "plastid"
+ tag "plastid/make_wiggle"
+
+ test("human chr20 bam - fiveprime_variable") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'SRX11780887' ], // meta map
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam", checkIfExists: true),
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam.bai", checkIfExists: true),
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/plastid/SRX11780887_p_offsets.txt", checkIfExists: true)
+ ]
+ input[1] = 'fiveprime_variable'
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert path(process.out.tracks.get(0).get(1).get(0)).getText().contains('track') },
+ { assert snapshot(process.out.versions).match() }
+ )
+ }
+ }
+
+ test("human chr20 bam - fiveprime_variable - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'SRX11780887' ], // meta map
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam", checkIfExists: true),
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam.bai", checkIfExists: true),
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/plastid/SRX11780887_p_offsets.txt", checkIfExists: true)
+ ]
+ input[1] = 'fiveprime_variable'
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert file(process.out.tracks.get(0).get(1).get(0)).exists() },
+ { assert snapshot(process.out.versions).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/plastid/make_wiggle/tests/main.nf.test.snap b/modules/nf-core/plastid/make_wiggle/tests/main.nf.test.snap
new file mode 100644
index 00000000..0d2f6778
--- /dev/null
+++ b/modules/nf-core/plastid/make_wiggle/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+ "human chr20 bam - fiveprime_variable": {
+ "content": [
+ [
+ "versions.yml:md5,4ecd455575ab11a0ad86dc5e0a6c6959"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.2",
+ "nextflow": "25.10.0"
+ },
+ "timestamp": "2025-12-10T12:36:00.352824"
+ },
+ "human chr20 bam - fiveprime_variable - stub": {
+ "content": [
+ [
+ "versions.yml:md5,4ecd455575ab11a0ad86dc5e0a6c6959"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.2",
+ "nextflow": "25.10.0"
+ },
+ "timestamp": "2025-12-10T12:26:10.353895"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/plastid/metagene_generate/environment.yml b/modules/nf-core/plastid/metagene_generate/environment.yml
new file mode 100644
index 00000000..86ff4ca2
--- /dev/null
+++ b/modules/nf-core/plastid/metagene_generate/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - plastid=0.6.1
diff --git a/modules/nf-core/plastid/metagene_generate/main.nf b/modules/nf-core/plastid/metagene_generate/main.nf
new file mode 100644
index 00000000..ef3faeaa
--- /dev/null
+++ b/modules/nf-core/plastid/metagene_generate/main.nf
@@ -0,0 +1,48 @@
+process PLASTID_METAGENE_GENERATE {
+ tag "$annotation"
+ label "process_low"
+
+ // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+ conda "${moduleDir}/environment.yml"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/plastid:0.6.1--py39had3e4b6_2':
+ 'biocontainers/plastid:0.6.1--py39had3e4b6_2' }"
+
+ input:
+ tuple val(meta), path(annotation)
+
+ output:
+ tuple val(meta), path("*_rois.txt"), emit: rois_txt
+ tuple val(meta), path("*_rois.bed"), emit: rois_bed
+ path "versions.yml", emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+ """
+ metagene generate \\
+ "${annotation.baseName}" \\
+ --annotation_files "$annotation" \\
+ $args
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ plastid: $VERSION
+ END_VERSIONS
+ """
+
+ stub:
+ def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+ """
+ touch ${annotation.baseName}_rois.txt
+ touch ${annotation.baseName}_rois.bed
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ plastid: $VERSION
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/plastid/metagene_generate/meta.yml b/modules/nf-core/plastid/metagene_generate/meta.yml
new file mode 100644
index 00000000..8034234a
--- /dev/null
+++ b/modules/nf-core/plastid/metagene_generate/meta.yml
@@ -0,0 +1,72 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "plastid_metagene_generate"
+description: Compute a metagene profile of read alignments, counts, or
+ quantitative data over one or more regions of interest, optionally
+ applying a mapping rule
+keywords:
+ - genomics
+ - riboseq
+ - psite
+tools:
+ - "plastid":
+ description: "Nucleotide-resolution analysis of next-generation sequencing and genomics data"
+ homepage: "https://github.com/joshuagryphon/plastid"
+ documentation: "https://plastid.readthedocs.io/en/latest/"
+ tool_dev_url: "https://github.com/joshuagryphon/plastid"
+ doi: "10.1186/s12864-016-3278-x"
+ licence: ["BSD-3-clause"]
+ identifier: biotools:plastid
+
+input:
+ - - meta:
+ type: map
+ description: |
+ Map containing reference information for the reference genome annotation file
+ e.g. `[ id:'Ensembl human v.111' ]`
+ - annotation:
+ type: file
+ description: annotation file of reference genome (BED, bigBed, GTF, GFF3)
+ pattern: "*.{bed,bigbed,gtf,gff3}"
+ ontologies:
+ - edam: http://edamontology.org/format_3003 # BED
+ - edam: http://edamontology.org/format_3004 # bigBed
+ - edam: http://edamontology.org/format_2306 # GTF
+ - edam: http://edamontology.org/format_1975 # GFF3
+output:
+ rois_txt:
+ - - meta:
+ type: map
+ description: |
+ Map containing reference information for the reference genome annotation file
+ e.g. `[ id:'Ensembl human v.111' ]`
+ - "*_rois.txt":
+ type: file
+ description: Tab-delimited text file describing the maximal spanning
+ window for each gene
+ pattern: "*_rois.txt"
+ ontologies: []
+ rois_bed:
+ - - meta:
+ type: map
+ description: |
+ Map containing reference information for the reference genome annotation file
+ e.g. `[ id:'Ensembl human v.111' ]`
+ - "*_rois.bed":
+ type: file
+ description: |
+ Maximal spanning windows in BED format for visualization in a genome
+ browser. The thickly-rendered portion of a window indicates its landmark.
+ pattern: "*_rois.bed"
+ ontologies:
+ - edam: http://edamontology.org/format_3003 # BED
+ versions:
+ - versions.yml:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ ontologies:
+ - edam: http://edamontology.org/format_3750 # YAML
+authors:
+ - "@suhrig"
+maintainers:
+ - "@suhrig"
diff --git a/modules/nf-core/plastid/metagene_generate/tests/main.nf.test b/modules/nf-core/plastid/metagene_generate/tests/main.nf.test
new file mode 100644
index 00000000..2f491337
--- /dev/null
+++ b/modules/nf-core/plastid/metagene_generate/tests/main.nf.test
@@ -0,0 +1,55 @@
+// nf-core modules test plastid
+nextflow_process {
+
+ name "Test Process PLASTID_METAGENE_GENERATE"
+ script "../main.nf"
+ process "PLASTID_METAGENE_GENERATE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "plastid"
+ tag "plastid/metagene_generate"
+
+ test("human chr20 gtf") {
+
+ when {
+ process {
+ """
+ input[0] = [[id:'homo_sapiens_chr20'], file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.111_chr20.gtf", checkIfExists: true)]
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert path(process.out.rois_txt.get(0).get(1)).getText().contains('ENSG') },
+ { assert path(process.out.rois_bed.get(0).get(1)).getText().contains('ENSG') },
+ { assert snapshot(process.out.versions).match('versions') }
+ )
+ }
+ }
+
+ test("human chr20 gtf -stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [[id:'homo_sapiens_chr20'], file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.111_chr20.gtf", checkIfExists: true)]
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert file(process.out.rois_txt.get(0).get(1)).exists() },
+ { assert file(process.out.rois_bed.get(0).get(1)).exists() },
+ { assert snapshot(process.out.versions).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/plastid/metagene_generate/tests/main.nf.test.snap b/modules/nf-core/plastid/metagene_generate/tests/main.nf.test.snap
new file mode 100644
index 00000000..9fd426fb
--- /dev/null
+++ b/modules/nf-core/plastid/metagene_generate/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+ "human chr20 gtf -stub": {
+ "content": [
+ [
+ "versions.yml:md5,3507c6516efe03f85ff066089c7a4b1b"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.2",
+ "nextflow": "25.10.0"
+ },
+ "timestamp": "2025-12-10T12:45:35.749835"
+ },
+ "versions": {
+ "content": [
+ [
+ "versions.yml:md5,3507c6516efe03f85ff066089c7a4b1b"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.3",
+ "nextflow": "25.10.0"
+ },
+ "timestamp": "2025-12-08T10:46:58.250416821"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/plastid/psite/environment.yml b/modules/nf-core/plastid/psite/environment.yml
new file mode 100644
index 00000000..86ff4ca2
--- /dev/null
+++ b/modules/nf-core/plastid/psite/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - plastid=0.6.1
diff --git a/modules/nf-core/plastid/psite/main.nf b/modules/nf-core/plastid/psite/main.nf
new file mode 100644
index 00000000..79389ce7
--- /dev/null
+++ b/modules/nf-core/plastid/psite/main.nf
@@ -0,0 +1,54 @@
+process PLASTID_PSITE {
+ tag "$meta.id"
+ label "process_single"
+
+ // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+ conda "${moduleDir}/environment.yml"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/plastid:0.6.1--py39had3e4b6_2':
+ 'biocontainers/plastid:0.6.1--py39had3e4b6_2' }"
+
+ input:
+ tuple val(meta), path(bam), path(bam_index)
+ tuple val(meta2), path(rois_txt)
+
+ output:
+ tuple val(meta), path("*_metagene_profiles.txt"), emit: metagene_profiles
+ tuple val(meta), path("*_p_offsets.png") , emit: p_offsets_png
+ tuple val(meta), path("*_p_offsets.txt") , emit: p_offsets
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def args = task.ext.args ?: ""
+ def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+ """
+ psite \
+ "$rois_txt" \\
+ "$prefix" \\
+ --count_files "$bam" \\
+ $args
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ plastid: $VERSION
+ END_VERSIONS
+ """
+
+ stub:
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+ """
+ touch ${prefix}_metagene_profiles.txt
+ touch ${prefix}_p_offsets.png
+ touch ${prefix}_p_offsets.txt
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ plastid: $VERSION
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/plastid/psite/meta.yml b/modules/nf-core/plastid/psite/meta.yml
new file mode 100644
index 00000000..cf0ec666
--- /dev/null
+++ b/modules/nf-core/plastid/psite/meta.yml
@@ -0,0 +1,94 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "plastid_psite"
+description: Estimate position of ribosomal P-site within ribosome profiling
+ read alignments as a function of read length
+keywords:
+ - genomics
+ - riboseq
+ - psite
+tools:
+ - "plastid":
+ description: "Nucleotide-resolution analysis of next-generation sequencing and genomics data"
+ homepage: "https://github.com/joshuagryphon/plastid"
+ documentation: "https://plastid.readthedocs.io/en/latest/"
+ tool_dev_url: "https://github.com/joshuagryphon/plastid"
+ doi: "10.1186/s12864-016-3278-x"
+ licence: ["BSD-3-clause"]
+ identifier: biotools:plastid
+
+input:
+ - - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - bam:
+ type: file
+ description: Genome BAM file
+ pattern: "*.bam"
+ ontologies:
+ - edam: http://edamontology.org/format_2572 # BAM
+ - bam_index:
+ type: file
+ description: Genome BAM index file
+ pattern: "*.bai"
+ ontologies:
+ - edam: http://edamontology.org/format_3327 # BAI
+ - - meta2:
+ type: map
+ description: |
+ Map containing reference information for the reference genome GTF file
+ e.g. `[ id:'Ensembl human v.111' ]`
+ - rois_txt:
+ type: file
+ description: |
+ Tab-delimited text file describing the maximal spanning
+ window for each gene (output from plastid_metagene_generate)
+ pattern: "*.txt"
+ ontologies: []
+output:
+ metagene_profiles:
+ - - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - "*_metagene_profiles.txt":
+ type: file
+ description: Matrix containing metagene profile for each read length
+ pattern: "*_metagene_profiles.txt"
+ ontologies: []
+ p_offsets_png:
+ - - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - "*_p_offsets.png":
+ type: file
+ description: Graphical illustration of metagene profiles
+ pattern: "*_p_offsets.png"
+ ontologies:
+ - edam: http://edamontology.org/format_3603 # PNG
+ p_offsets:
+ - - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - "*_p_offsets.txt":
+ type: file
+ description: Selected p-site offset for each read length
+ pattern: "*_p_offsets.txt"
+ ontologies: []
+ versions:
+ - versions.yml:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ ontologies:
+ - edam: http://edamontology.org/format_3750 # YAML
+authors:
+ - "@suhrig"
+maintainers:
+ - "@suhrig"
diff --git a/modules/nf-core/plastid/psite/tests/main.nf.test b/modules/nf-core/plastid/psite/tests/main.nf.test
new file mode 100644
index 00000000..a7b78ff9
--- /dev/null
+++ b/modules/nf-core/plastid/psite/tests/main.nf.test
@@ -0,0 +1,67 @@
+// nf-core modules test plastid
+nextflow_process {
+
+ name "Test Process PLASTID_PSITE"
+ script "../main.nf"
+ process "PLASTID_PSITE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "plastid"
+ tag "plastid/psite"
+
+ test("human chr20 bam") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'SRX11780887' ], // meta map
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam", checkIfExists: true),
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam.bai", checkIfExists: true)
+ ]
+ input[1] = [[id:'homo_sapiens_chr20'], file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/plastid/Homo_sapiens.GRCh38.111_chr20_rois.txt", checkIfExists: true)]
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert path(process.out.metagene_profiles.get(0).get(1)).getText().contains('28-mers') },
+ { assert file(process.out.p_offsets_png.get(0).get(1)).exists() },
+ { assert path(process.out.p_offsets.get(0).get(1)).getText().contains("length\tp_offset") },
+ { assert snapshot(process.out.versions).match() }
+ )
+ }
+ }
+
+ test("human chr20 bam -stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'SRX11780887' ], // meta map
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam", checkIfExists: true),
+ file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam.bai", checkIfExists: true)
+ ]
+ input[1] = [[id:'homo_sapiens_chr20'], file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/plastid/Homo_sapiens.GRCh38.111_chr20_rois.txt", checkIfExists: true)]
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert file(process.out.metagene_profiles.get(0).get(1)).exists() },
+ { assert file(process.out.p_offsets_png.get(0).get(1)).exists() },
+ { assert file(process.out.p_offsets.get(0).get(1)).exists() },
+ { assert snapshot(process.out.versions).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/plastid/psite/tests/main.nf.test.snap b/modules/nf-core/plastid/psite/tests/main.nf.test.snap
new file mode 100644
index 00000000..c2a3532c
--- /dev/null
+++ b/modules/nf-core/plastid/psite/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+ "human chr20 bam -stub": {
+ "content": [
+ [
+ "versions.yml:md5,f0a577bc6782d64582ef1c52b5b47ad7"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.2",
+ "nextflow": "25.10.0"
+ },
+ "timestamp": "2025-12-10T12:46:13.713244"
+ },
+ "human chr20 bam": {
+ "content": [
+ [
+ "versions.yml:md5,f0a577bc6782d64582ef1c52b5b47ad7"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.2",
+ "nextflow": "25.10.0"
+ },
+ "timestamp": "2025-12-10T12:46:07.654842"
+ }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index eb233255..7218b21c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -90,20 +90,28 @@ params {
skip_multiqc = false
// Riboseq module-specific options
- skip_ribotish = false
- extra_ribotish_quality_args = null
- extra_ribotish_predict_args = null
- skip_ribotricer = false
- extra_ribotricer_prepareorfs_args = null
- extra_ribotricer_detectorfs_args = null
- skip_ribowaltz = false
- extra_ribowaltz_args = null
- extra_anota2seq_run_args = null
- translational_efficiency_method = 'anota2seq'
- extra_deltate_args = null
- te_lfc_threshold = 0.2630344 // log2(1.2) - anota2seq default
- rna_lfc_threshold = 0 // 0 = disabled
- ribo_lfc_threshold = 0 // 0 = disabled
+ skip_ribotish = false
+ extra_ribotish_quality_args = null
+ extra_ribotish_predict_args = null
+ skip_ribotricer = false
+ extra_ribotricer_prepareorfs_args = null
+ extra_ribotricer_detectorfs_args = null
+ skip_ribowaltz = false
+ extra_ribowaltz_args = null
+ extra_anota2seq_run_args = null
+ translational_efficiency_method = 'anota2seq'
+ extra_deltate_args = null
+ te_lfc_threshold = 0.2630344 // log2(1.2) - anota2seq default
+ rna_lfc_threshold = 0 // 0 = disabled
+ ribo_lfc_threshold = 0 // 0 = disabled
+ skip_plastid = false
+ plastid_min_length = 15
+ plastid_max_length = 50
+ plastid_default_psite_offset = 12
+ extra_plastid_metagene_generate_args = null
+ extra_plastid_psite_args = null
+ extra_plastid_make_wiggle_args = null
+
// Read length equalisation
equalise_read_lengths = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index abcdd58b..c7b42112 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -488,6 +488,35 @@
"description": "Minimum absolute log2 fold change for translated mRNA (Ribo-seq) to be considered significant. Set to 0 to disable. Maps to anota2seq selDeltaP / deltaTE lfc_threshold_ribo.",
"fa_icon": "fas fa-ruler-vertical"
},
+ "extra_plastid_metagene_generate_args": {
+ "type": "string",
+ "description": "Extra arguments to pass to plastid/metagene_generate command in addition to defaults defined by the pipeline."
+ },
+ "extra_plastid_psite_args": {
+ "type": "string",
+ "description": "Extra arguments to pass to plastid/psite command in addition to defaults defined by the pipeline."
+ },
+ "extra_plastid_make_wiggle_args": {
+ "type": "string",
+ "description": "Extra arguments to pass to plastid/make_wiggle command in addition to defaults defined by the pipeline."
+ },
+ "plastid_min_length": {
+ "type": "integer",
+ "default": 15,
+ "fa_icon": "fas fa-ruler-horizontal",
+ "description": "Plastid only considers reads of at least the given length."
+ },
+ "plastid_max_length": {
+ "type": "integer",
+ "default": 50,
+ "fa_icon": "fas fa-ruler-horizontal",
+ "description": "Plastid only considers reads of at most the given length."
+ },
+ "plastid_default_psite_offset": {
+ "type": "integer",
+ "default": 12,
+ "description": "Default p-site offset to use for read lengths where the offset cannot be determined automatically from the data."
+ },
"equalise_read_lengths": {
"type": "boolean",
"default": false,
@@ -641,6 +670,11 @@
"type": "boolean",
"description": "Skip riboWaltz.",
"fa_icon": "fas fa-fast-forward"
+ },
+ "skip_plastid": {
+ "type": "boolean",
+ "description": "Skip plastid.",
+ "fa_icon": "fas fa-fast-forward"
}
}
},
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index e9bfb1c2..e46a3d5f 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
"datePublished": "2025-12-03T16:26:32+00:00",
- "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/riboseq)\n[](https://github.com/nf-core/riboseq/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/riboseq/actions/workflows/linting.yml)[](https://nf-co.re/riboseq/results)[](https://doi.org/10.5281/zenodo.10966364)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/riboseq)\n\n[](https://nfcore.slack.com/channels/riboseq)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/riboseq** is a bioinformatics pipeline for analysis of Ribo-seq data. It borrows heavily from nf-core/rnaseq in the preprocessing stages:\n\n\n\n1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))\n2. Sub-sample FastQ files and auto-infer strandedness ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))\n3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n4. UMI extraction ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))\n5. Adapter and quality trimming ([`Trim Galore!`](https://github.com/FelixKrueger/TrimGalore))\n6. Removal of genome contaminants ([`BBSplit`](http://seqanswers.com/forums/showthread.php?t=41288))\n7. Removal of ribosomal RNA ([`SortMeRNA`](https://github.com/biocore/sortmerna))\n8. Genome alignment of reads, outputting both genome and transcriptome alignments with [`STAR`](https://github.com/alexdobin/STAR)\n9. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n10. UMI-based deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))\n\nDifferences occur in the downstream analysis steps. Currently these specialist steps are:\n\n1. Check reads distribution around annotated protein coding regions on user provided transcripts, show frame bias and estimate P-site offset for different group of reads ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))\n2. (default, optional) Predict translated open reading frames and/ or translation initiation sites _de novo_ from alignment data ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))\n3. (default, optional) Derive candidate ORFs from reference data and detect translated ORFs from that list ([`Ribotricer`](https://github.com/smithlabcode/ribotricer))\n4. (default, optional) Derive P-sites and QC from transcriptome alignments ([`riboWaltz`](https://github.com/LabTranslationalArchitectomics/riboWaltz))\n5. (optional) Use a translational efficiency approach to study the dynamics of transcription and translation, with [anota2seq](https://bioconductor.org/packages/release/bioc/html/anota2seq.html). **requires matched RNA-seq and Ribo-seq data**\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,strandedness,type\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward,riboseq\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end). Each row should have a 'type' value of `riboseq`, `tiseq` or `rnaseq`. Future iterations of the workflow will conduct paired analysis of matched riboseq and rnaseq samples to accomplish analysis types such as 'translational efficiency, but in the current version you should set this to `riboseq` or `tiseq` for reglar Ribo-seq or TI-seq data respectively.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/riboseq \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n### Including a translational efficiency analysis\n\n\n\nIn the translational efficiency analysis provided by [anota2seq](https://bioconductor.org/packages/release/bioc/html/anota2seq.html), we use matched pairs of Ribo-seq and RNA-seq data to study the relationship between transcription and translation as they differ between two treatment groups. For example the test data for this workflow has a contrasts file like:\n\n```csv\nid,variable,reference,target,batch,pair\ntreated_vs_control,treatment,control,treated,,pair\n```\n\nThis describes how to compare groups of samples between treament groups, and between RNA-seq and Ribo-seq. In order the columns are:\n\n- `id`: a unique identifier to use for the contrast\n- 'variable`: which vaiable (column) of the sample sheet should be used to separate the treatment groups?\n- `reference`: which value of the variable column should be used to select samples to be used as the reference/ base group?\n- `target`: which value of the variable column should be used to select samples to be used as the target/treated group?\n- `batch`: (optional) specify a variable in the sample sheet that defines sample batches\n- `pair`: (optional) specify a variable in the sample sheet that defines sample pairing between RNA-seq and Ribo-seq samples. If not specified, it is assumed that the two types of sample are ordered the same.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/riboseq/usage) and the [parameter documentation](https://nf-co.re/riboseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/riboseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/riboseq/output).\n\n## Credits\n\nnf-core/riboseq was originally written by [Jonathan Manning](https://github.com/pinin4fjords) (Bioinformatics Engineer at Seqera) with support from [Altos Labs](https://www.altoslabs.com/) and in discussion with [Felix Krueger](https://github.com/FelixKrueger) and [Christel Krueger](https://github.com/ChristelKrueger). We thank the following people for their input:\n\n- Anne Bresciani (ZS)\n- [Felipe Almeida](https://github.com/fmalmeida) (ZS)\n- [Mikhail Osipovitch](https://github.com/mosi223) (ZS)\n- [Edward Wallace](https://github.com/ewallace) (University of Edinburgh)\n- [Jack Tierney](https://github.com/JackCurragh) (University College Cork)\n- [Maxime U Garcia](https://github.com/maxulysse) (Seqera)\n- [Ira A Iosub](https://github.com/iraiosub) (The Francis Crick Institute)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#riboseq` channel](https://nfcore.slack.com/channels/riboseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/riboseq for your analysis, please cite it using the following doi: [10.5281/zenodo.10966364](https://doi.org/10.5281/zenodo.10966364)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
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