First version of pridepy download module

modules/bigbio/pridepy/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::pridepy=0.0.14

modules/bigbio/pridepy/main.nf

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+process PRIDEPY_DOWNLOAD {
+    tag "${meta.id}"
+    label 'process_low'
+    label 'process_long'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/pridepy:0.0.14--pyhdfd78af_0'
+        : 'biocontainers/pridepy:0.0.14--pyhdfd78af_0'}"
+
+    input:
+    val(meta)
+
+    output:
+    tuple val(meta), path("*.{raw,mzML,mzML.gz,mgf,d.tar,d.tar.gz,d.zip,dia,wiff,wiff.scan}"), emit: spectra,   optional: true
+    tuple val(meta), path("*-checksum.tsv"),                                                   emit: checksums, optional: true
+    path "versions.yml",                                                                       emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    pridepy ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pridepy: \$(python -c "from importlib.metadata import version; print(version('pridepy'))" || echo "unknown")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def checksum_touch = args.contains('--checksum-check') ? "touch \"${meta.id}-checksum.tsv\"" : ''
+    """
+    touch "${meta.id}.raw"
+    ${checksum_touch}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pridepy: 0.0.14
+    END_VERSIONS
+    """
+}

modules/bigbio/pridepy/meta.yml

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+name: pridepy
+description: Python client for PRIDE Archive — download and query proteomics datasets
+keywords:
+  - pride
+  - download
+  - proteomics
+  - raw files
+  - globus
+  - aspera
+tools:
+  - pridepy:
+      description: |
+        pridepy is a Python client for the PRIDE Archive REST API.
+        It supports downloading public/private files via FTP, Aspera, Globus (HTTPS), or S3,
+        as well as querying project metadata and file listings.
+        The specific sub-command and arguments are passed via task.ext.args.
+      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 task information.
+        e.g. `[ id: 'PXD001819' ]`
+output:
+  spectra:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing task information forwarded from input.
+      - "*.{raw,mzML,mzML.gz,mgf,d.tar,d.tar.gz,d.zip,dia,wiff,wiff.scan}":
+          type: file
+          description: |
+            Mass spectrometry spectra files downloaded from PRIDE Archive
+            (Thermo .raw, mzML, Bruker .d archives, DIA-NN .dia, Sciex .wiff, etc.).
+            Emitted to the task workDir; downstream pipelines pick specific files
+            via publishDir / saveAs in their modules.config.
+          pattern: "*.{raw,mzML,mzML.gz,mgf,d.tar,d.tar.gz,d.zip,dia,wiff,wiff.scan}"
+  checksums:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing task information forwarded from input.
+      - "*-checksum.tsv":
+          type: file
+          description: SHA1 checksums file generated by pridepy when --checksum-check is enabled.
+          pattern: "*-checksum.tsv"
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+authors:
+  - "@ypriverol"
+maintainers:
+  - "@ypriverol"

modules/bigbio/pridepy/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process PRIDEPY_DOWNLOAD"
+    script "../main.nf"
+    process "PRIDEPY_DOWNLOAD"
+    tag "modules"
+    tag "modules_bigbio"
+    tag "modules_pridepy"
+    tag "pridepy"
+
+    test("Should run stub mode (no checksum)") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ id: 'PXD001819' ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.out.spectra.size() == 1
+            assert process.out.checksums.size() == 0
+            assert snapshot(
+                process.out.spectra,
+                process.out.versions
+            ).match("stub_no_checksum")
+        }
+    }
+
+    test("Should run stub mode with --checksum-check") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ id: 'PXD001819' ]
+                """
+            }
+            params {
+                module_args = '--checksum-check'
+            }
+            config "./nextflow.config"
+        }
+
+        then {
+            assert process.success
+            assert process.out.spectra.size() == 1
+            assert process.out.checksums.size() == 1
+            assert snapshot(
+                process.out.spectra,
+                process.out.checksums,
+                process.out.versions
+            ).match("stub_with_checksum")
+        }
+    }
+}

modules/bigbio/pridepy/tests/main.nf.test.snap

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+{
+    "stub_no_checksum": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "PXD001819"
+                    },
+                    "PXD001819.raw:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,c27ccb04c91f92f188b7f4cf2d54ed49"
+            ]
+        ],
+        "timestamp": "2026-04-28T18:15:37.876014654",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "stub_with_checksum": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "PXD001819"
+                    },
+                    "PXD001819.raw:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "PXD001819"
+                    },
+                    "PXD001819-checksum.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,c27ccb04c91f92f188b7f4cf2d54ed49"
+            ]
+        ],
+        "timestamp": "2026-04-28T18:15:43.996367071",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}

modules/bigbio/pridepy/tests/nextflow.config

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+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'PRIDEPY_DOWNLOAD' {
+        ext.args = { params.module_args ?: '' }
+    }
+}