New module: parsesdrf/convert

modules/nf-core/sdrfpipelines/parsesdrf/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:
+  - "bioconda::sdrf-pipelines=0.1.3"

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

@@ -0,0 +1,33 @@
+process SDRFPIPELINES_PARSESDRF {
+    tag "${sdrf.baseName}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.1.3--pyhdfd78af_0':
+        'quay.io/biocontainers/sdrf-pipelines:0.1.3--pyhdfd78af_0' }"
+
+    input:
+    path sdrf
+
+    output:
+    path "samplesheet.tsv"   , emit: samplesheet
+    path "search_presets.tsv", emit: search_presets
+    tuple val("${task.process}"), val('sdrf-pipelines'), eval("parse_sdrf --version | cut -d ' ' -f 2"), topic: versions, emit: versions_sdrfpipelines
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    parse_sdrf $args \\
+        -s ${sdrf}
+    """
+
+    stub:
+    """
+    touch samplesheet.tsv
+    touch search_presets.tsv
+    """
+}

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

@@ -0,0 +1,77 @@
+name: "sdrfpipelines_parsesdrf"
+description: |
+  Parse and convert an SDRF (Sample and Data Relationship Format) file into
+  pipeline-specific samplesheet/configuration files using the sdrf-pipelines
+  `parse_sdrf` CLI. The conversion subcommand (e.g. `convert-mhcquant`,
+  `convert-openms`) and its output flags are supplied via `task.ext.args`.
+keywords:
+  - sdrf
+  - samplesheet
+  - proteomics
+  - immunopeptidomics
+  - metadata
+tools:
+  - "sdrf-pipelines":
+      description: "A set of tools to validate and convert SDRF files for proteomics
+        pipelines."
+      homepage: "https://github.com/bigbio/sdrf-pipelines"
+      documentation: "https://github.com/bigbio/sdrf-pipelines"
+      tool_dev_url: "https://github.com/bigbio/sdrf-pipelines"
+      doi: "10.1021/acs.jproteome.1c00505"
+      licence:
+        - "Apache-2.0"
+      identifier: "biotools:sdrf-pipelines"
+input:
+  - sdrf:
+      type: file
+      description: SDRF file describing the experimental design and sample
+        metadata.
+      pattern: "*.{tsv,sdrf.tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475
+output:
+  samplesheet:
+    - "samplesheet.tsv":
+        type: file
+        description: |
+          Samplesheet derived from the SDRF file. The exact contents depend on
+          the conversion subcommand passed via `ext.args` (e.g. mhcquant-style
+          samplesheet when `convert-mhcquant` is used).
+        pattern: "samplesheet.tsv"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+  search_presets:
+    - "search_presets.tsv":
+        type: file
+        description: |
+          Search parameter presets derived from the SDRF file (one row per
+          unique search configuration). Produced by subcommands that emit a
+          presets file, e.g. `convert-mhcquant`.
+        pattern: "search_presets.tsv"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+  versions_sdrfpipelines:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "sdrf-pipelines":
+          type: string
+          description: The name of the tool
+      - "parse_sdrf --version | cut -d ' ' -f 2":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "sdrf-pipelines":
+          type: string
+          description: The name of the tool
+      - "parse_sdrf --version | cut -d ' ' -f 2":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@jonasscheid"
+maintainers:
+  - "@jonasscheid"

modules/nf-core/sdrfpipelines/parsesdrf/tests/main.nf.test

@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process SDRFPIPELINES_PARSESDRF"
+    script "../main.nf"
+    process "SDRFPIPELINES_PARSESDRF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sdrfpipelines"
+    tag "sdrfpipelines/parsesdrf"
+
+    config "./nextflow.config"
+
+    test("sdrf - mhcquant - PXD009752") {
+
+        when {
+            process {
+                """
+                input[0] = file('https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/PXD009752.sdrf.tsv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sdrf - mhcquant - PXD009752 - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file('https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/PXD009752.sdrf.tsv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/sdrfpipelines/parsesdrf/tests/main.nf.test.snap

@@ -0,0 +1,76 @@
+{
+    "sdrf - mhcquant - PXD009752 - stub": {
+        "content": [
+            {
+                "0": [
+                    "samplesheet.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "search_presets.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    [
+                        "SDRFPIPELINES_PARSESDRF",
+                        "sdrf-pipelines",
+                        "0.1.3"
+                    ]
+                ],
+                "samplesheet": [
+                    "samplesheet.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "search_presets": [
+                    "search_presets.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions_sdrfpipelines": [
+                    [
+                        "SDRFPIPELINES_PARSESDRF",
+                        "sdrf-pipelines",
+                        "0.1.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-04T09:45:05.072262669",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sdrf - mhcquant - PXD009752": {
+        "content": [
+            {
+                "0": [
+                    "samplesheet.tsv:md5,4d7d2f1ca8d3def75b05ae8c01c481d8"
+                ],
+                "1": [
+                    "search_presets.tsv:md5,3ba3b5c24f71025bfc1799ea87cd0a12"
+                ],
+                "2": [
+                    [
+                        "SDRFPIPELINES_PARSESDRF",
+                        "sdrf-pipelines",
+                        "0.1.3"
+                    ]
+                ],
+                "samplesheet": [
+                    "samplesheet.tsv:md5,4d7d2f1ca8d3def75b05ae8c01c481d8"
+                ],
+                "search_presets": [
+                    "search_presets.tsv:md5,3ba3b5c24f71025bfc1799ea87cd0a12"
+                ],
+                "versions_sdrfpipelines": [
+                    [
+                        "SDRFPIPELINES_PARSESDRF",
+                        "sdrf-pipelines",
+                        "0.1.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-04T09:44:47.41878644",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}

modules/nf-core/sdrfpipelines/parsesdrf/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: "SDRFPIPELINES_PARSESDRF" {
+        ext.args = "convert-mhcquant -os samplesheet.tsv -op search_presets.tsv"
+    }
+}