Merge branch 'master' into pypgx/runngspipeline

nf-core · Jan 10, 2025 · 593d9c2 · 593d9c2
2 parents 069ae20 + f349d93
commit 593d9c2
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diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -17,7 +17,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+    - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
       with:
         distribution: "temurin"
         java-version: "17"
@@ -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()

diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
diff --git a/.github/skip_nf_test.json b/.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"
+    ]
+}
diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -74,14 +74,14 @@ jobs:
 
   nf-test-gpu:
     runs-on: "gpu"
-    name: "GPU | ${{ matrix.profile }} | ${{ matrix.shard }}"
+    name: "GPU Test | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: nf-test-changes
     if: ${{ needs.nf-test-changes.outputs.modules != '[]' || needs.nf-test-changes.outputs.subworkflows != '[]' }}
     strategy:
       fail-fast: false
       matrix:
         shard: [1, 2]
-        profile: [docker_self_hosted, singularity] # conda?
+        profile: [docker_self_hosted, singularity]
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: 2
@@ -103,18 +103,23 @@ 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()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |