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plastid metagene_generate, make_wiggle, psite (#9482)
* plastid metagene_generate, make_wiggle, psite * pair BAM and BAI files * pair bam and p_offsets * omit optional arguments * metagene generate accepts various input formats * add meta * do not remove variable headers from output files * warning about hard-coded version * make lint happy * make lint happy #2 * plastid/make_wiggle: nf-core standards compliance - Add mapping_rule val input (enum: fiveprime, threeprime, center, fiveprime_variable) - Move output_format to ext.args (optional arg per nf-core standards) - Add validation: error if p_offsets missing with fiveprime_variable - Remove hardcoded --fiveprime_variable - Update meta.yml with mapping_rule input and enum - Update tests with mapping_rule input 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * adapt meta.yml to new parameters * plastid: consolidate test snapshots and fix reproducibility - Consolidate multiple snapshot assertions into single snapshots per test - Remove snapshots of empty stub files (just check existence) - Exclude non-reproducible PNG from psite snapshots (matplotlib drift) - Format metagene_generate command across multiple lines 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * plastid/make_wiggle: remove tracks from snapshot Wig files have non-reproducible md5sums across environments. Content is already validated via getText().contains('track'). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * plastid/psite: remove non-reproducible outputs from snapshot metagene_profiles.txt and p_offsets.txt have non-reproducible md5sums. Content is already validated via getText().contains() checks. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
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‎modules/nf-core/plastid/make_wiggle/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- plastid=0.6.1

‎modules/nf-core/plastid/make_wiggle/main.nf‎

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process PLASTID_MAKE_WIGGLE {
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tag "$meta.id"
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label "process_single"
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plastid:0.6.1--py39had3e4b6_2':
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'biocontainers/plastid:0.6.1--py39had3e4b6_2' }"
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input:
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tuple val(meta), path(bam), path(bam_index), path(p_offsets)
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val(mapping_rule)
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output:
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tuple val(meta), path("*.{wig,bedgraph}"), emit: tracks
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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if (mapping_rule == 'fiveprime_variable' && !p_offsets) {
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error "p_offsets file is required when using mapping_rule 'fiveprime_variable'"
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}
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def prefix = task.ext.prefix ?: "${meta.id}"
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def args = task.ext.args ?: ""
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def offset_arg = mapping_rule == 'fiveprime_variable' ? "--offset $p_offsets" : ""
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def extension = args.contains('--output_format bedgraph') ? "bedgraph" : "wig"
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def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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make_wiggle \\
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--count_files "$bam" \\
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$offset_arg \\
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--${mapping_rule} \\
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-o "$prefix" \\
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$args
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if [ "$extension" = "bedgraph" ]; then
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for FILE in *.wig; do
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mv "\$FILE" "\${FILE%.wig}.bedgraph"
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done
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plastid: $VERSION
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END_VERSIONS
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"""
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stub:
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if (mapping_rule == 'fiveprime_variable' && !p_offsets) {
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error "p_offsets file is required when using mapping_rule 'fiveprime_variable'"
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}
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def prefix = task.ext.prefix ?: "${meta.id}"
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def args = task.ext.args ?: ""
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def extension = args.contains('--output_format bedgraph') ? "bedgraph" : "wig"
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def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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touch ${prefix}_fw.${extension}
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touch ${prefix}_rc.${extension}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plastid: $VERSION
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END_VERSIONS
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"""
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}

‎modules/nf-core/plastid/make_wiggle/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "plastid_make_wiggle"
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description: Create wiggle or bedGraph files from alignment files after applying
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a read mapping rule (e.g. to map ribosome-protected footprints at their
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P-sites), for visualization in a genome browser
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keywords:
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- genomics
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- riboseq
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- psite
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- wiggle
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- bedgraph
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tools:
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- "plastid":
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description: "Nucleotide-resolution analysis of next-generation sequencing and
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genomics data"
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homepage: "https://github.com/joshuagryphon/plastid"
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documentation: "https://plastid.readthedocs.io/en/latest/"
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tool_dev_url: "https://github.com/joshuagryphon/plastid"
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doi: "10.1186/s12864-016-3278-x"
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licence: ["BSD-3-clause"]
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identifier: biotools:plastid
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- bam:
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type: file
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description: Genome BAM file
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pattern: "*.bam"
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ontologies:
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- edam: http://edamontology.org/format_2572 # BAM
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- bam_index:
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type: file
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description: Genome BAM index file
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pattern: "*.bai"
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ontologies:
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- edam: http://edamontology.org/format_3327 # BAI
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- p_offsets:
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type: file
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description: |
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Selected p-site offset for each read length (output from plastid_psite).
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Required when mapping_rule is 'fiveprime_variable', otherwise pass empty list [].
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pattern: "*_p_offsets.txt"
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ontologies: []
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- mapping_rule:
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type: string
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description: |
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Read mapping rule. Use 'fiveprime_variable' with p_offsets file to map reads to P-sites.
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enum: ["fiveprime", "threeprime", "center", "fiveprime_variable"]
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output:
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tracks:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- "*.{wig,bedgraph}":
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type: file
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description: wig/bedgraph tracks for forward and reverse strands
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pattern: "*.{wig,bedgraph}"
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ontologies:
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- edam: http://edamontology.org/format_3005 # wig
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- edam: http://edamontology.org/format_3583 # bedgraph
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versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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authors:
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- "@suhrig"
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maintainers:
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- "@suhrig"

‎modules/nf-core/plastid/make_wiggle/tests/main.nf.test‎

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// nf-core modules test plastid
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nextflow_process {
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name "Test Process PLASTID_MAKE_WIGGLE"
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script "../main.nf"
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process "PLASTID_MAKE_WIGGLE"
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tag "modules"
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tag "modules_nfcore"
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tag "plastid"
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tag "plastid/make_wiggle"
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test("human chr20 bam - fiveprime_variable") {
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when {
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process {
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"""
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input[0] = [
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[ id:'SRX11780887' ], // meta map
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam.bai", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/plastid/SRX11780887_p_offsets.txt", checkIfExists: true)
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]
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input[1] = 'fiveprime_variable'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert path(process.out.tracks.get(0).get(1).get(0)).getText().contains('track') },
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{ assert snapshot(process.out.versions).match() }
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)
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}
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}
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test("human chr20 bam - fiveprime_variable - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'SRX11780887' ], // meta map
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887_chr20.bam.bai", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/plastid/SRX11780887_p_offsets.txt", checkIfExists: true)
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]
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input[1] = 'fiveprime_variable'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert file(process.out.tracks.get(0).get(1).get(0)).exists() },
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{ assert snapshot(process.out.versions).match() }
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)
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}
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}
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}

‎modules/nf-core/plastid/make_wiggle/tests/main.nf.test.snap‎

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{
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"human chr20 bam - fiveprime_variable": {
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"content": [
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[
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"versions.yml:md5,4ecd455575ab11a0ad86dc5e0a6c6959"
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-10T12:36:00.352824"
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},
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"human chr20 bam - fiveprime_variable - stub": {
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"content": [
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[
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"versions.yml:md5,4ecd455575ab11a0ad86dc5e0a6c6959"
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-10T12:26:10.353895"
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}
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}

‎modules/nf-core/plastid/metagene_generate/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- plastid=0.6.1

‎modules/nf-core/plastid/metagene_generate/main.nf‎

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process PLASTID_METAGENE_GENERATE {
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tag "$annotation"
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label "process_low"
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plastid:0.6.1--py39had3e4b6_2':
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'biocontainers/plastid:0.6.1--py39had3e4b6_2' }"
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input:
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tuple val(meta), path(annotation)
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output:
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tuple val(meta), path("*_rois.txt"), emit: rois_txt
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tuple val(meta), path("*_rois.bed"), emit: rois_bed
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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metagene generate \\
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"${annotation.baseName}" \\
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--annotation_files "$annotation" \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plastid: $VERSION
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END_VERSIONS
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"""
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stub:
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def VERSION = "0.6.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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touch ${annotation.baseName}_rois.txt
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touch ${annotation.baseName}_rois.bed
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plastid: $VERSION
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END_VERSIONS
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"""
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}

‎modules/nf-core/plastid/metagene_generate/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "plastid_metagene_generate"
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description: Compute a metagene profile of read alignments, counts, or
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quantitative data over one or more regions of interest, optionally
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applying a mapping rule
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keywords:
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- genomics
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- riboseq
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- psite
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tools:
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- "plastid":
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description: "Nucleotide-resolution analysis of next-generation sequencing and genomics data"
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homepage: "https://github.com/joshuagryphon/plastid"
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documentation: "https://plastid.readthedocs.io/en/latest/"
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tool_dev_url: "https://github.com/joshuagryphon/plastid"
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doi: "10.1186/s12864-016-3278-x"
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licence: ["BSD-3-clause"]
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identifier: biotools:plastid
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input:
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- - meta:
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type: map
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description: |
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Map containing reference information for the reference genome annotation file
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e.g. `[ id:'Ensembl human v.111' ]`
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- annotation:
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type: file
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description: annotation file of reference genome (BED, bigBed, GTF, GFF3)
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pattern: "*.{bed,bigbed,gtf,gff3}"
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ontologies:
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- edam: http://edamontology.org/format_3003 # BED
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- edam: http://edamontology.org/format_3004 # bigBed
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- edam: http://edamontology.org/format_2306 # GTF
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- edam: http://edamontology.org/format_1975 # GFF3
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output:
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rois_txt:
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- - meta:
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type: map
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description: |
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Map containing reference information for the reference genome annotation file
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e.g. `[ id:'Ensembl human v.111' ]`
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- "*_rois.txt":
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type: file
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description: Tab-delimited text file describing the maximal spanning
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window for each gene
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pattern: "*_rois.txt"
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ontologies: []
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rois_bed:
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- - meta:
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type: map
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description: |
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Map containing reference information for the reference genome annotation file
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e.g. `[ id:'Ensembl human v.111' ]`
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- "*_rois.bed":
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type: file
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description: |
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Maximal spanning windows in BED format for visualization in a genome
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browser. The thickly-rendered portion of a window indicates its landmark.
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pattern: "*_rois.bed"
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ontologies:
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- edam: http://edamontology.org/format_3003 # BED
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versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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authors:
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- "@suhrig"
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maintainers:
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- "@suhrig"

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