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plastid metagene_generate, make_wiggle, psite
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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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- bioconda::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 "$meta.id"
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label "process_single"
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plastid:0.6.1--py39had3e4b6_2':
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'biocontainers/plastid:0.6.1--py39had3e4b6_2' }"
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input:
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tuple val(meta), path(bam)
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tuple val(meta2), path(bam_index)
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tuple val(meta3), path(p_offsets)
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val min_length
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val output_format
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val fiveprime_variable
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output:
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tuple val(meta), path("*.{wig,bedgraph}"), emit: tracks
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def prefix = task.ext.prefix ?: "${meta.id}"
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def extension = output_format == "bedgraph" ? "bedgraph" : "wig"
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def args = task.ext.args ?: ""
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if (fiveprime_variable) args += "--fiveprime_variable"
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"""
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make_wiggle \\
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--count_files "$bam" \\
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--offset "$p_offsets" \\
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--min_length "$min_length" \\
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--output_format "$output_format" \\
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--verbose \\
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-o "$prefix" \\
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$args
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sed -i '/^##/d' *.wig # remove variable comment header
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if [ "$output_format" = "bedgraph" ]; then
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for FILE in *.wig; do
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mv "\$FILE" "\${FILE%.wig}.bedgraph"
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done
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plastid: 0.6.1
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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def extension = output_format == "bedgraph" ? "bedgraph" : "wig"
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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: 0.6.1
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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
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applying a read mapping rule (e.g. to map ribosome-protected footprints at
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their 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 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: "http://dx.doi.org/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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- - meta2:
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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_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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- - meta3:
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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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- p_offsets:
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type: file
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description: Selected p-site offset for each read length (output from plastid_psites)
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pattern: "*_p_offsets.txt"
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ontologies: []
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- min_length:
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type: integer
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description: Minimum length of reads to consider
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- output_format:
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type: string
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description: `variable_step` or `bedgraph`
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- fiveprime_variable:
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type: boolean
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description: |
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Map read alignment to a variable offset from 5' position of read, with
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offset determined by read length
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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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- "*.${extension}":
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type: file
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description: wig/bedgraph tracks for forward and reverse strands
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pattern: "*.${extension}"
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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") {
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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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]
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input[1] = [
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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.bai", checkIfExists: true)
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]
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input[2] = [
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[ id:'SRX11780887' ], // meta map
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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[3] = 23 // min_length
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input[4] = 'variable_step' // output_format
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input[5] = true // 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 snapshot(process.out.tracks).match('wig') },
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{ assert snapshot(process.out.versions).match('versions') }
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)
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}
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}
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test("human chr20 bam -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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]
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input[1] = [
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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.bai", checkIfExists: true)
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]
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input[2] = [
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[ id:'SRX11780887' ], // meta map
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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[3] = 23 // min_length
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input[4] = 'variable_step' // output_format
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input[5] = true // 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 snapshot(process.out.tracks).match('wig_stub') },
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{ assert snapshot(process.out.versions).match('versions_stub') }
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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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"versions_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": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-01T08:21:20.834995954"
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},
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"wig": {
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"content": [
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[
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[
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{
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"id": "SRX11780887"
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},
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[
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"SRX11780887_fw.wig:md5,647f8b1b990e3a7f13f761bad68646fe",
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"SRX11780887_rc.wig:md5,17955523d22a9d9bc67a39228cdda343"
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]
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]
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]
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-01T08:21:14.597903696"
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},
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"versions": {
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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": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-01T08:21:14.614712687"
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},
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"wig_stub": {
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"content": [
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[
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[
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{
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"id": "SRX11780887"
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},
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[
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"SRX11780887_fw.wig:md5,d41d8cd98f00b204e9800998ecf8427e",
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"SRX11780887_rc.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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]
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]
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-01T08:21:20.817255625"
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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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- bioconda::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 "$gtf"
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label "process_low"
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plastid:0.6.1--py39had3e4b6_2':
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'biocontainers/plastid:0.6.1--py39had3e4b6_2' }"
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input:
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path gtf
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val landmark
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output:
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path "*_rois.txt" , emit: rois_txt
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path "*_rois.bed" , emit: rois_bed
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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metagene generate "${gtf.baseName}" --landmark "$landmark" --annotation_files "$gtf" $args
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sed -i '/^##/d' *_rois.* # remove variable comment header
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plastid: 0.6.1
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END_VERSIONS
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"""
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stub:
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"""
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touch ${gtf.baseName}_rois.txt
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touch ${gtf.baseName}_rois.bed
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plastid: 0.6.1
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END_VERSIONS
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"""
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}

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