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jonasscheidclaudeLouisLeNezet
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New module: parsesdrf/convert (#11514)
* feat(sdrfpipelines/parsesdrf): add module to convert SDRF files via sdrf-pipelines Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * refactor(sdrfpipelines/convertmhcquant): rename from parsesdrf, lock to convert-mhcquant subcommand, add meta map and prefix-based outputs Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * fix(sdrfpipelines/convertmhcquant): restore versions emit name and align meta.yml output patterns with main.nf prefix Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * refactor(parsesdrf/convert): generalize to all parse_sdrf convert-* subcommands with per-format output tuples * fix(parsesdrf/convert): resolve CI failures, default module_args per-test, emit versions topic, bump sdrf-pipelines 0.1.3->0.1.4 Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * fix(parsesdrf/convert): drop md5s from maxquant snapshot (non-deterministic XML output upstream) Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * test(parsesdrf/convert): wrap process.out in sanitizeOutput across all tests to drop duplicate numeric channel keys (-40% snap size, md5 coverage unchanged) Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Update modules/nf-core/parsesdrf/convert/environment.yml Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> * feat(parsesdrf/convert): promote fasta/raw_folder to input channel, drop module_args plumbing Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
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‎modules/nf-core/parsesdrf/convert/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::sdrf-pipelines=0.1.4

‎modules/nf-core/parsesdrf/convert/main.nf‎

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process PARSESDRF_CONVERT {
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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 "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.1.4--pyhdfd78af_0':
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'quay.io/biocontainers/sdrf-pipelines:0.1.4--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(sdrf), path(fasta), val(raw_folder)
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val format
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output:
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tuple val(meta), path("${prefix}_samplesheet.tsv"), path("${prefix}_presets.tsv"), emit: mhcquant, optional: true
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tuple val(meta), path("${prefix}_samplesheet.tsv"), path("${prefix}_experimental_design.tsv"), emit: openms, optional: true
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tuple val(meta), path("${prefix}.xml"), path("${prefix}_design.txt"), emit: maxquant, optional: true
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tuple val(meta), path("${prefix}.csv"), emit: msstats, optional: true
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tuple val(meta), path("${prefix}_design.csv"), path("${prefix}_comparisons.csv"), emit: normalyzerde, optional: true
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tuple val(meta), path("${prefix}.cfg"), path("${prefix}_design.tsv"), emit: diann, optional: true
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tuple val("${task.process}"), val('sdrf-pipelines'), eval("parse_sdrf --version | cut -d ' ' -f 2"), topic: versions, emit: versions_sdrfpipelines
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when:
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task.ext.when == null || task.ext.when
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script:
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prefix = task.ext.prefix ?: "${meta.id}"
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def args = task.ext.args ?: ''
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def output_args = ''
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def post = ''
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if (format == 'mhcquant') {
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output_args = "-os ${prefix}_samplesheet.tsv -op ${prefix}_presets.tsv"
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} else if (format == 'openms') {
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// convert-openms writes openms.tsv + (optionally) experimental_design.tsv
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post = "mv openms.tsv ${prefix}_samplesheet.tsv ; [ -f experimental_design.tsv ] && mv experimental_design.tsv ${prefix}_experimental_design.tsv || true"
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} else if (format == 'maxquant') {
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if (!fasta || !raw_folder) {
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error "PARSESDRF_CONVERT: format 'maxquant' requires both `fasta` (path) and `raw_folder` (string) inputs"
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}
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// fasta is staged into the work dir; raw_folder is a literal string embedded into mqpar.xml's <filePaths>
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output_args = "-f ${fasta} -r ${raw_folder} -o1 ${prefix}.xml -o2 ${prefix}_design.txt"
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} else if (format == 'msstats') {
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output_args = "-o ${prefix}.csv"
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} else if (format == 'normalyzerde') {
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output_args = "-o ${prefix}_design.csv -oc ${prefix}_comparisons.csv"
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} else if (format == 'diann') {
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// convert-diann writes diann_config.cfg + diann_design.tsv with fixed names
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post = "mv diann_config.cfg ${prefix}.cfg && mv diann_design.tsv ${prefix}_design.tsv"
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} else {
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error "PARSESDRF_CONVERT: unsupported format '${format}' (expected one of: mhcquant, openms, maxquant, msstats, normalyzerde, diann)"
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}
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"""
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parse_sdrf convert-${format} \\
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-s ${sdrf} \\
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${output_args} \\
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${args}
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${post}
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"""
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stub:
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prefix = task.ext.prefix ?: "${meta.id}"
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def stub_files
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if (format == 'mhcquant') {
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stub_files = ["${prefix}_samplesheet.tsv", "${prefix}_presets.tsv"]
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} else if (format == 'openms') {
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stub_files = ["${prefix}_samplesheet.tsv", "${prefix}_experimental_design.tsv"]
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} else if (format == 'maxquant') {
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stub_files = ["${prefix}.xml", "${prefix}_design.txt"]
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} else if (format == 'msstats') {
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stub_files = ["${prefix}.csv"]
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} else if (format == 'normalyzerde') {
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stub_files = ["${prefix}_design.csv", "${prefix}_comparisons.csv"]
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} else if (format == 'diann') {
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stub_files = ["${prefix}.cfg", "${prefix}_design.tsv"]
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} else {
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error "PARSESDRF_CONVERT: unsupported format '${format}'"
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}
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def touches = stub_files.collect { f -> "touch ${f}" }.join('\n ')
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"""
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${touches}
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"""
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}

‎modules/nf-core/parsesdrf/convert/meta.yml‎

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name: "parsesdrf_convert"
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description: |
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Convert an SDRF (Sample and Data Relationship Format) file into a
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pipeline-specific samplesheet/configuration using the `parse_sdrf
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convert-<format>` subcommands of the sdrf-pipelines package. The chosen
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`format` selects the subcommand; the module owns the output filenames and
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emits one tuple per supported format (mhcquant, openms, maxquant, msstats,
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normalyzerde, diann).
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keywords:
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- sdrf
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- sdrf-pipelines
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- samplesheet
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- proteomics
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- immunopeptidomics
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- mhcquant
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- openms
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- maxquant
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- msstats
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- normalyzerde
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- diann
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- metadata
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tools:
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- "sdrf-pipelines":
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description: "A set of tools to validate and convert SDRF files for proteomics
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pipelines."
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homepage: "https://github.com/bigbio/sdrf-pipelines"
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documentation: "https://github.com/bigbio/sdrf-pipelines"
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tool_dev_url: "https://github.com/bigbio/sdrf-pipelines"
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doi: "10.1021/acs.jproteome.1c00505"
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licence:
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- "Apache-2.0"
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identifier: "biotools:sdrf-pipelines"
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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/run information
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e.g. `[ id:'PXD009752' ]`
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- sdrf:
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type: file
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description: SDRF file describing the experimental design and sample metadata.
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pattern: "*.{tsv,sdrf.tsv}"
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ontologies:
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- edam: http://edamontology.org/format_3475
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- fasta:
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type: file
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description: |
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Protein database FASTA. Required when `format == 'maxquant'`
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(passed to `-f`); pass `[]` otherwise.
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pattern: "*.{fasta,fa,fasta.gz,fa.gz}"
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ontologies:
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- edam: http://edamontology.org/format_1929
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- raw_folder:
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type: string
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description: |
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Directory prefix embedded as a literal string into the
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`<filePaths>` block of the generated MaxQuant `mqpar.xml`; must
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resolve on the host that later runs MaxQuant. Required when
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`format == 'maxquant'`; pass `''` otherwise.
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- format:
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type: string
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description: |
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Target converter. One of: `mhcquant`, `openms`, `maxquant`,
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`msstats`, `normalyzerde`, `diann`. Selects the
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`parse_sdrf convert-<format>` subcommand.
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output:
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mhcquant:
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- - meta:
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type: map
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description: Groovy Map containing sample/run information
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- "${prefix}_samplesheet.tsv":
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type: file
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description: MHCquant samplesheet TSV (`-os`).
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pattern: "*_samplesheet.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475
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- "${prefix}_presets.tsv":
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type: file
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description: MHCquant search-preset TSV (`-op`).
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pattern: "*_presets.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475
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openms:
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- - meta:
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type: map
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description: Groovy Map containing sample/run information
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- "${prefix}_samplesheet.tsv":
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type: file
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description: OpenMS samplesheet TSV (renamed from `openms.tsv`).
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pattern: "*_samplesheet.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475
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- "${prefix}_experimental_design.tsv":
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type: file
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description: OpenMS experimental design TSV.
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pattern: "*_experimental_design.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475
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maxquant:
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- - meta:
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type: map
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description: Groovy Map containing sample/run information
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- "${prefix}.xml":
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type: file
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description: MaxQuant `mqpar.xml` (`-o1`).
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pattern: "*.xml"
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ontologies:
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- edam: http://edamontology.org/format_2332
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- "${prefix}_design.txt":
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type: file
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description: MaxQuant experimental design TXT (`-o2`).
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pattern: "*_design.txt"
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ontologies:
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- edam: http://edamontology.org/format_3475
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msstats:
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- - meta:
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type: map
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description: Groovy Map containing sample/run information
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- "${prefix}.csv":
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type: file
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description: MSstats annotation CSV (`-o`).
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pattern: "*.csv"
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ontologies:
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- edam: http://edamontology.org/format_3752
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normalyzerde:
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- - meta:
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type: map
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description: Groovy Map containing sample/run information
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- "${prefix}_design.csv":
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type: file
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description: NormalyzerDE design CSV (`-o`).
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pattern: "*_design.csv"
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ontologies:
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- edam: http://edamontology.org/format_3752
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- "${prefix}_comparisons.csv":
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type: file
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description: NormalyzerDE comparisons CSV (`-oc`).
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pattern: "*_comparisons.csv"
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ontologies:
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- edam: http://edamontology.org/format_3752
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diann:
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- - meta:
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type: map
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description: Groovy Map containing sample/run information
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- "${prefix}.cfg":
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type: file
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description: DIA-NN config (renamed from `diann_config.cfg`).
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pattern: "*.cfg"
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ontologies:
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- edam: http://edamontology.org/format_2330
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- "${prefix}_design.tsv":
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type: file
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description: DIA-NN experimental design TSV (renamed from `diann_design.tsv`).
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pattern: "*_design.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475
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versions_sdrfpipelines:
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- - "${task.process}":
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type: string
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description: The name of the process
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- "sdrf-pipelines":
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type: string
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description: The name of the tool
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- "parse_sdrf --version | cut -d ' ' -f 2":
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - "${task.process}":
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type: string
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description: The name of the process
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- "sdrf-pipelines":
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type: string
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description: The name of the tool
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- "parse_sdrf --version | cut -d ' ' -f 2":
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@jonasscheid"
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maintainers:
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- "@jonasscheid"

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