try to fix ci.yml

genomic-medicine-sweden · Oct 13, 2024 · 8ade5fd · 8ade5fd
1 parent 75587fb
commit 8ade5fd
Showing 1 changed file with 17 additions and 5 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -29,11 +29,23 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
         test_name:
-           - "test"
+          - "test"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
         parameters:
-          - ""
-          - " --skip_subsample_region true --skip_downsample true --skip_build_tracks true --skip_stringtie true --skip_vep true --skip_drop_ae true --skip_drop_as true"
+          - "-profile test,docker"
+          - "-profile test,docker --skip_subsample_region true --skip_downsample true --skip_build_tracks true --skip_stringtie true --skip_vep true --skip_drop_ae true --skip_drop_as true"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -71,6 +83,6 @@ jobs:
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.parameters }}"
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.test_name }} ${{ matrix.parameters }} --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results