Merge branch 'master' into scds

.github/actions/nf-test-action/action.yml

@@ -83,12 +83,39 @@ runs:
           --filter process,workflow \
           ${{ inputs.paths }}
 
-      # TODO If no test.tap, then make one to spoof?
-    - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
-      if: ${{ inputs.path != '' }}
-      with:
-        path: >-
-          test.tap
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+
+    - name: Generate test summary
+      if: always()
+      shell: bash
+      run: |
+        # Add header if it doesn't exist (using a token file to track this)
+        if [ ! -f ".summary_header" ]; then
+          echo "# 🚀 nf-test Results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+          touch .summary_header
+        fi
+
+        if [ -f test.tap ]; then
+          while IFS= read -r line; do
+            if [[ $line =~ ^ok ]]; then
+              test_name="${line#ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            elif [[ $line =~ ^not\ ok ]]; then
+              test_name="${line#not ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            fi
+          done < test.tap
+        else
+          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+        fi
 
     - name: Clean up
       if: always()

.github/skip_nf_test.json

@@ -0,0 +1,93 @@
+{
+    "conda": [
+        "modules/nf-core/angsd/gl",
+        "modules/nf-core/annotsv/installannotations",
+        "modules/nf-core/backsub",
+        "modules/nf-core/bakta/bakta",
+        "modules/nf-core/bakta/baktadbdownload",
+        "modules/nf-core/bases2fastq",
+        "modules/nf-core/bcl2fastq",
+        "modules/nf-core/bclconvert",
+        "modules/nf-core/celesta",
+        "modules/nf-core/cellpose",
+        "modules/nf-core/cellranger/count",
+        "modules/nf-core/cellranger/mkfastq",
+        "modules/nf-core/cellranger/mkgtf",
+        "modules/nf-core/cellranger/mkref",
+        "modules/nf-core/cellranger/mkvdjref",
+        "modules/nf-core/cellranger/multi",
+        "modules/nf-core/cellranger/vdj",
+        "modules/nf-core/cellrangerarc/mkgtf",
+        "modules/nf-core/checkqc",
+        "modules/nf-core/custom/dumpsoftwareversions",
+        "modules/nf-core/deepcell/mesmer",
+        "modules/nf-core/deepsomatic",
+        "modules/nf-core/deepvariant",
+        "modules/nf-core/deepvariant/callvariants",
+        "modules/nf-core/deepvariant/makeexamples",
+        "modules/nf-core/deepvariant/postprocessvariants",
+        "modules/nf-core/deepvariant/rundeepvariant",
+        "modules/nf-core/deepvariant/vcfstatsreport",
+        "modules/nf-core/doubletdetection",
+        "modules/nf-core/ensemblvep/vep",
+        "modules/nf-core/fastk/fastk",
+        "modules/nf-core/fastk/histex",
+        "modules/nf-core/fastk/merge",
+        "modules/nf-core/fcs/fcsadaptor",
+        "modules/nf-core/fcs/fcsgx",
+        "modules/nf-core/ganon/buildcustom",
+        "modules/nf-core/ganon/classify",
+        "modules/nf-core/ganon/report",
+        "modules/nf-core/ganon/table",
+        "modules/nf-core/gatk4/cnnscorevariants",
+        "modules/nf-core/gatk4/determinegermlinecontigploidy",
+        "modules/nf-core/genescopefk",
+        "modules/nf-core/happy/sompy",
+        "modules/nf-core/ilastik/multicut",
+        "modules/nf-core/ilastik/pixelclassification",
+        "modules/nf-core/imputeme/vcftoprs",
+        "modules/nf-core/islandpath",
+        "modules/nf-core/mcquant",
+        "modules/nf-core/mcstaging/imc2mc",
+        "modules/nf-core/mcstaging/phenoimager2mc",
+        "modules/nf-core/merquryfk/katcomp",
+        "modules/nf-core/merquryfk/katgc",
+        "modules/nf-core/merquryfk/merquryfk",
+        "modules/nf-core/merquryfk/ploidyplot",
+        "modules/nf-core/molkartgarage/clahe",
+        "modules/nf-core/parabricks",
+        "modules/nf-core/quartonotebook",
+        "modules/nf-core/scimap/mcmicro",
+        "modules/nf-core/scimap/spatiallda",
+        "modules/nf-core/sentieon/bwaindex",
+        "modules/nf-core/sentieon/bwamem",
+        "modules/nf-core/sentieon/datametrics",
+        "modules/nf-core/sentieon/dedup",
+        "modules/nf-core/sentieon/qualcal",
+        "modules/nf-core/spaceranger/count",
+        "modules/nf-core/spaceranger/mkgtf",
+        "modules/nf-core/spaceranger/mkref",
+        "modules/nf-core/spotiflow",
+        "modules/nf-core/svanalyzer/svbenchmark",
+        "modules/nf-core/universc",
+        "modules/nf-core/vt/decompose",
+        "modules/nf-core/wittyer",
+        "modules/nf-core/xeniumranger/import-segmentation",
+        "modules/nf-core/xeniumranger/relabel",
+        "modules/nf-core/xeniumranger/rename",
+        "modules/nf-core/xeniumranger/resegment",
+        "subworkflows/nf-core/bcl_demultiplex",
+        "subworkflows/nf-core/deepvariant",
+        "subworkflows/nf-core/fasta_newick_epang_gappa",
+        "subworkflows/nf-core/fastq_align_bamcmp_bwa",
+        "subworkflows/nf-core/fastq_align_bwa",
+        "subworkflows/nf-core/vcf_annotate_ensemblvep"
+    ],
+    "docker_self_hosted": ["modules/nf-core/parabricks"],
+    "singularity": [
+        "modules/nf-core/bases2fastq",
+        "modules/nf-core/deepsomatic",
+        "modules/nf-core/parabricks",
+        "modules/nf-core/universc"
+    ]
+}

.github/workflows/gpu-tests.yml

@@ -103,7 +103,7 @@ jobs:
           total_shards: ${{ env.TOTAL_SHARDS }}
           paths: "${{ join(fromJson(needs.nf-test-changes.outputs.paths), ' ') }}"
 
-  confirm-pass:
+  confirm-pass-gpu:
     runs-on: ubuntu-latest
     needs: [nf-test-gpu]
     if: always()

.github/workflows/nf-test.yml

@@ -92,7 +92,45 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           fetch-depth: 0
+
+      - name: Filter paths
+        id: filter
+        run: |
+          PATHS='${{ needs.nf-test-changes.outputs.paths }}'
+          FILTERED=$(jq -n -c \
+            --arg profile "${{ matrix.profile }}" \
+            --argjson input_paths "$PATHS" \
+            '
+            def get_skip_list: inputs | .[$profile] // [];
+
+            # Get skip list and filter
+            get_skip_list as $skip_patterns |
+
+            # Debug output
+            ($skip_patterns | "Skip patterns: " + (map("  - " + .) | join(","))) |
+            debug |
+
+            # Do the actual filtering
+            $input_paths | map(
+              . as $path |
+              select($skip_patterns | all(. as $pattern | ($path | startswith($pattern)) | not))
+            ) as $result |
+
+            # Debug what was skipped
+            (if ($input_paths - $result) | length > 0 then
+              "Skipped: " + (($input_paths - $result) | map("  - " + .) | join(","))
+            else
+              "No paths skipped"
+            end) |
+            debug |
+
+            $result
+            ' .github/skip_nf_test.json)
+
+          echo "filtered_paths=${FILTERED}" >> $GITHUB_OUTPUT
+
       - name: Run nf-test Action
+        if: ${{steps.filter.outputs.filtered_paths != '[]'}}
         uses: ./.github/actions/nf-test-action
         env:
           SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
@@ -103,7 +141,7 @@ jobs:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
-          paths: "${{ join(fromJson(needs.nf-test-changes.outputs.paths), ' ') }}"
+          paths: "${{ join(fromJson(steps.filter.outputs.filtered_paths), ' ') }}"
 
   confirm-pass:
     runs-on: ubuntu-latest