Merge branch 'main' into ci/tests

stjudecloud · Nov 25, 2024 · d70e05f · d70e05f
2 parents fa97539 + 75a640b
commit d70e05f
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Showing 11 changed files with 7 additions and 471 deletions.
diff --git a/.github/workflows/docker-build.yaml b/.github/workflows/docker-build.yaml
@@ -18,7 +18,7 @@ jobs:
           fetch-depth: 0
       - name: set matrix
         id: set-matrix
-        run: echo "images=$(find docker -maxdepth 2 -mindepth 2 -not -path "*/cellranger/*" | jq --raw-input --slurp --compact-output 'split("\n")[:-1]')" >> $GITHUB_OUTPUT
+        run: echo "images=$(find docker -maxdepth 2 -mindepth 2 | jq --raw-input --slurp --compact-output 'split("\n")[:-1]')" >> $GITHUB_OUTPUT
 
   build-images:
     needs: list-images

diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
@@ -12,7 +12,7 @@ jobs:
           uses: actions/checkout@v4
         - name: set tags
           id: set-tags
-          run: echo "tags=$(find tests -name '*.yaml' -exec yq --output-format yaml '.[].tags[] ' {} \;| sort | uniq | grep -vE 'deprecated|miniwdl|cellranger' | jq -ncR '[inputs]')" >> $GITHUB_OUTPUT
+          run: echo "tags=$(find tests -name '*.yaml' -exec yq --output-format yaml '.[].tags[] ' {} \;| sort | uniq | grep -vE 'deprecated|miniwdl' | jq -ncR '[inputs]')" >> $GITHUB_OUTPUT
   pytest_check:
     needs: list-tags
     runs-on: ubuntu-latest
@@ -33,7 +33,7 @@ jobs:
         pip install -r requirements-dev.txt
     - name: filter tests
       run: |
-        find tests -name '*.yaml' -exec yq --output-format yaml -i 'del(.[] | select(.tags[] | test("reference|deprecated|cellranger") ) )' {} \;
+        find tests -name '*.yaml' -exec yq --output-format yaml -i 'del(.[] | select(.tags[] | test("reference|deprecated") ) )' {} \;
     - name: Run pytest-workflow
       run: |
-        pytest --git-aware --basetemp /home/runner/work/pytest --symlink --tag ${{ matrix.tag }}
+        pytest --git-aware --basetemp /home/runner/work/pytest --symlink --tag ${{ matrix.tag }}
diff --git a/.github/workflows/sprocket-check.yaml b/.github/workflows/sprocket-check.yaml
@@ -10,4 +10,4 @@ jobs:
         - name: Run sprocket
           uses: stjude-rust-labs/sprocket-action@main
           with:
-            exclude-patterns: template,scrnaseq,cellranger
+            exclude-patterns: template
diff --git a/.github/workflows/sprocket-lint.yaml b/.github/workflows/sprocket-lint.yaml
@@ -11,7 +11,7 @@ jobs:
           uses: stjude-rust-labs/sprocket-action@main
           with:
             lint: true
-            exclude-patterns: template,scrnaseq,cellranger
+            exclude-patterns: template
             deny-warnings: true
             deny-notes: true
-            except: TrailingComma,ContainerValue
+            except: TrailingComma,ContainerValue
diff --git a/docker/cellranger/1.1.1/Dockerfile b/docker/cellranger/1.1.1/Dockerfile
diff --git a/tests/input/pbmc_1k_v3.tar.gz b/tests/input/pbmc_1k_v3.tar.gz
diff --git a/tests/tools/input_json/cellranger_count.json b/tests/tools/input_json/cellranger_count.json
diff --git a/tests/tools/test_cellranger.yaml b/tests/tools/test_cellranger.yaml
diff --git a/tools/cellranger.wdl b/tools/cellranger.wdl