Add module to fetch SDRF files from PRIDE Archive

modules/nf-core/pridepy/fetchsdrf/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::pridepy=0.0.15"

modules/nf-core/pridepy/fetchsdrf/main.nf

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+process PRIDEPY_FETCHSDRF {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pridepy:0.0.15--pyhdfd78af_0':
+        'quay.io/biocontainers/pridepy:0.0.15--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), val(pride_id)
+
+    output:
+    tuple val(meta), path("${prefix}.sdrf.tsv"), emit: sdrf
+    tuple val("${task.process}"), val('pridepy'), eval('python -c "from importlib.metadata import version; print(version(\'pridepy\'))"'), topic: versions, emit: versions_pridepy
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    pridepy stream-files-metadata \\
+        -a "${pride_id}" \\
+        -o files_metadata.json \\
+        $args
+
+    # Check if SDRF is present in metadata and extract
+    sdrf_name=\$(awk -F'"' '/"fileName" *: *"(sdrf\\.tsv|[^"]+\\.sdrf\\.tsv)"/ {print \$4; exit}' files_metadata.json)
+    [ -n "\$sdrf_name" ] || { echo "ERROR: No SDRF file found for ${pride_id}" >&2; exit 1; }
+
+    pridepy download-file-by-name \\
+        -a "${pride_id}" \\
+        -f "\$sdrf_name" \\
+        -o . \\
+        $args
+
+    mv "\$sdrf_name" "${prefix}.sdrf.tsv"
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.sdrf.tsv
+    """
+}

modules/nf-core/pridepy/fetchsdrf/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pridepy_fetchsdrf"
+description: Fetch an SDRF file from the PRIDE Archive for a given project accession.
+keywords:
+  - pride
+  - sdrf
+  - proteomics
+  - download
+  - metadata
+tools:
+  - "pridepy":
+      description: |
+        Python client library to access PRIDE Archive data programmatically,
+        including downloading files and metadata for public proteomics datasets.
+      homepage: "https://github.com/PRIDE-Archive/pridepy"
+      documentation: "https://github.com/PRIDE-Archive/pridepy"
+      tool_dev_url: "https://github.com/PRIDE-Archive/pridepy"
+      licence: ["Apache-2.0"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'PXD004684' ]`
+    - pride_id:
+        type: string
+        description: PRIDE Archive project accession (e.g. PXD004684)
+
+output:
+  sdrf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'PXD004684' ]`
+      - "${prefix}.sdrf.tsv":
+          type: file
+          description: SDRF (Sample and Data Relationship Format) file describing the experimental design of the PRIDE project
+          pattern: "*.sdrf.tsv"
+  versions_pridepy:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - pridepy:
+          type: string
+          description: The tool name
+      - 'python -c "from importlib.metadata import version; print(version(''pridepy''))"':
+          type: string
+          description: The command used to generate the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - pridepy:
+          type: string
+          description: The tool name
+      - 'python -c "from importlib.metadata import version; print(version(''pridepy''))"':
+          type: string
+          description: The command used to generate the version of the tool
+
+authors:
+  - "@jonasscheid"
+maintainers:
+  - "@jonasscheid"

modules/nf-core/pridepy/fetchsdrf/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process PRIDEPY_FETCHSDRF"
+    script "../main.nf"
+    process "PRIDEPY_FETCHSDRF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pridepy"
+    tag "pridepy/fetchsdrf"
+
+    test("pride - PXD004684") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'PXD004684' ],
+                    'PXD004684'
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.sdrf[0][1]).text.contains('Source Name') },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("pride - PXD004684 - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'PXD004684' ],
+                    'PXD004684'
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/pridepy/fetchsdrf/tests/main.nf.test.snap

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+{
+    "pride - PXD004684 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "PXD004684"
+                        },
+                        "PXD004684.sdrf.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "PRIDEPY_FETCHSDRF",
+                        "pridepy",
+                        "0.0.15"
+                    ]
+                ],
+                "sdrf": [
+                    [
+                        {
+                            "id": "PXD004684"
+                        },
+                        "PXD004684.sdrf.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_pridepy": [
+                    [
+                        "PRIDEPY_FETCHSDRF",
+                        "pridepy",
+                        "0.0.15"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-04T07:51:07.096175717",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "pride - PXD004684": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "PXD004684"
+                        },
+                        "PXD004684.sdrf.tsv:md5,a8a2aa91d85adb241110fe3a7ce8f372"
+                    ]
+                ],
+                "1": [
+                    [
+                        "PRIDEPY_FETCHSDRF",
+                        "pridepy",
+                        "0.0.15"
+                    ]
+                ],
+                "sdrf": [
+                    [
+                        {
+                            "id": "PXD004684"
+                        },
+                        "PXD004684.sdrf.tsv:md5,a8a2aa91d85adb241110fe3a7ce8f372"
+                    ]
+                ],
+                "versions_pridepy": [
+                    [
+                        "PRIDEPY_FETCHSDRF",
+                        "pridepy",
+                        "0.0.15"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-04T07:50:51.643144802",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}