ci: Update module_name filter step

.github/scripts/get_module_path.js

@@ -0,0 +1,110 @@
+// Test this locally with:
+// node .github/scripts/get_module_path.js
+
+// Core functionality that processes the file paths
+function get_module_names(filter_modules_files) {
+    return [
+        ...new Set(
+            filter_modules_files.map((path) =>
+                path
+                    .replace("tests/", "")
+                    .replace("modules/nf-core/", "")
+                    .split("/")
+                    .slice(0, 2)
+                    .filter(
+                        (x) =>
+                            !x.startsWith("main.nf") &&
+                            x !== "tests" &&
+                            x !== "meta.yml" &&
+                            x !== "environment.yml" &&
+                            !x.endsWith(".snap") &&
+                            !x.endsWith(".config")
+                    )
+                    .join("/")
+            )
+        ),
+    ];
+}
+
+// GitHub Actions entry point
+function run({ github, context }) {
+    try {
+        // Debug logging
+        console.log('Context payload:', context.payload);
+        console.log('Input files:', context.payload.inputs?.files);
+
+        // Get the files from the context and ensure it's a valid JSON string
+        let files;
+        if (typeof context.payload.inputs?.files === "string") {
+            console.log('Processing string input');
+            files = JSON.parse(context.payload.inputs.files);
+        } else if (Array.isArray(context.payload.inputs?.files)) {
+            console.log('Processing array input');
+            files = context.payload.inputs.files;
+        } else {
+            console.log('No valid input found, defaulting to empty array');
+            files = [];
+        }
+
+        console.log('Files to process:', files);
+        const result = get_module_names(files);
+        console.log('Processed result:', result);
+
+        // Ensure we're returning a properly formatted JSON string
+        const jsonResult = JSON.stringify(result);
+        console.log('Final JSON output:', jsonResult);
+        return jsonResult;
+    } catch (error) {
+        console.error("Error processing module paths:", error);
+        console.error("Error details:", {
+            errorName: error.name,
+            errorMessage: error.message,
+            errorStack: error.stack
+        });
+        return "[]";
+    }
+}
+
+// Test cases
+function runTests() {
+    const test_case_1 = [
+        "modules/nf-core/umicollapse/tests/main.nf.test",
+        "modules/nf-core/umicollapse/tests/main.nf.test.snap",
+        "modules/nf-core/umicollapse/tests/nextflow.config",
+        "modules/nf-core/umicollapse/tests/nextflow_PE.config",
+        "modules/nf-core/umicollapse/tests/nextflow_SE.config",
+        "modules/nf-core/umitools/dedup/tests/main.nf.test",
+        "modules/nf-core/umitools/dedup/tests/main.nf.test.snap",
+        "modules/nf-core/umitools/dedup/main.nf",
+    ];
+    const result_1 = ["umicollapse", "umitools/dedup"];
+
+    const test_case_2 = [
+        "modules/nf-core/mafft/align/environment.yml",
+        "modules/nf-core/mafft/align/main.nf",
+        "modules/nf-core/mafft/align/meta.yml",
+        "modules/nf-core/mafft/align/tests/main.nf.test",
+        "modules/nf-core/mafft/align/tests/main.nf.test.snap",
+        "modules/nf-core/mafft/guidetree/environment.yml",
+        "modules/nf-core/mafft/guidetree/main.nf",
+        "modules/nf-core/mafft/guidetree/meta.yml",
+        "modules/nf-core/mafft/guidetree/tests/main.nf.test",
+        "modules/nf-core/mafft/guidetree/tests/main.nf.test.snap",
+        "tests/modules/nf-core/epang/split/main.nf",
+    ];
+    const result_2 = ["mafft/align", "mafft/guidetree", "epang/split"];
+
+    console.assert(JSON.stringify(get_module_names(test_case_1)) === JSON.stringify(result_1), "Test case 1 failed");
+    console.assert(JSON.stringify(get_module_names(test_case_2)) === JSON.stringify(result_2), "Test case 2 failed");
+
+    console.log("All tests passed!");
+}
+
+// Handle different execution contexts
+if (require.main === module) {
+    // Script was run directly (node get_module_path.js)
+    runTests();
+} else {
+    // Script was imported/required
+    module.exports = run;
+}

.github/workflows/lint.yml

@@ -77,30 +77,31 @@ jobs:
         uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
         id: module_names
         with:
+          result-encoding: string
           script: |
-            return [...new Set(${{ steps.filter.outputs.modules_files }}
-              .map(path => path
-                .replace('modules/nf-core/', '')
-                .split('/')
-                .slice(0, 2)
-                .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml')
-                .join('/'))
-              )
-            ];
+            const script = require('./.github/scripts/get_module_path.js')
+            console.log('Raw modules_files:', '${{ steps.filter.outputs.modules_files }}')
+            const files = JSON.parse('${{ steps.filter.outputs.modules_files }}')
+            console.log('Parsed files:', files)
+            const result = script({ github, context: { payload: { inputs: { files } } } })
+            console.log('Result:', result)
+            return result
+
       - name: debug
         run: |
-          echo ${{ steps.filter.outputs.modules_files }}
-          echo ${{ steps.module_names.outputs.result }}
+          echo "Modules files: ${{ steps.filter.outputs.modules_files }}"
+          echo "Module names: ${{ fromJson(steps.module_names.outputs.result) }}"
+          echo "Raw module names output: ${{ steps.module_names.outputs.result }}"
 
   nf-core-lint-modules:
     runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
     name: nf-core lint modules
     needs: nf-core-changes
-    if: ${{ (needs.nf-core-changes.outputs.modules == 'true') }}
+    if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' && needs.nf-core-changes.outputs.modules_files != '' }}
     strategy:
       fail-fast: false
       matrix:
-        module: "${{ fromJson(needs.nf-core-changes.outputs.modules_files) }}"
+        module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }}
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 

modules/nf-core/upd/tests/nextflow.config

@@ -1,3 +1,3 @@
 process {
-    ext.args = { "--proband earlycasualcaiman --father hugelymodelbat --mother slowlycivilbuck --af-tag AF regions"  }
+    ext.args = { "--proband earlycasualcaiman --father hugelymodelbat --mother slowlycivilbuck --af-tag AF regions" }
 }