fix(pridepy): drop output/ subdir, write to workDir

modules/bigbio/pridepy/main.nf

@@ -12,20 +12,17 @@ process PRIDEPY_DOWNLOAD {
     val(meta)
 
     output:
-    tuple val(meta), path("output/"), emit: download_dir
-    path "versions.yml",              emit: versions
+    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 ?: ''
     """
-    mkdir -p output
-    (
-        cd output
-        pridepy ${args}
-    )
+    pridepy ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -34,9 +31,11 @@ process PRIDEPY_DOWNLOAD {
     """
 
     stub:
+    def args = task.ext.args ?: ''
+    def checksum_touch = args.contains('--checksum-check') ? "touch \"${meta.id}-checksum.tsv\"" : ''
     """
-    mkdir -p output
-    touch "output/${meta.id}.placeholder"
+    touch "${meta.id}.raw"
+    ${checksum_touch}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/bigbio/pridepy/meta.yml

@@ -27,15 +27,28 @@ input:
         Groovy Map containing task information.
         e.g. `[ id: 'PXD001819' ]`
 output:
-  download_dir:
+  spectra:
     - - meta:
           type: map
           description: |
             Groovy Map containing task information forwarded from input.
-      - "output/":
-          type: directory
-          description: Directory containing downloaded files (for download sub-commands)
-          pattern: "output/"
+      - "*.{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

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

@@ -8,7 +8,7 @@ nextflow_process {
     tag "modules_pridepy"
     tag "pridepy"
 
-    test("Should run stub mode") {
+    test("Should run stub mode (no checksum)") {
 
         options "-stub"
 
@@ -22,7 +22,40 @@ nextflow_process {
 
         then {
             assert process.success
-            assert snapshot(process.out.versions).match("versions_stub")
+            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

@@ -1,11 +1,47 @@
 {
-    "versions_stub": {
+    "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": "2026-04-28T14:06:27.317530521",
+        "timestamp": "2026-04-28T18:15:43.996367071",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

modules/bigbio/pridepy/tests/nextflow.config

@@ -1,3 +1,7 @@
 process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'PRIDEPY_DOWNLOAD' {
+        ext.args = { params.module_args ?: '' }
+    }
 }