ci: Upload logs on failures

.github/workflows/bowtie_align.yml

@@ -14,29 +14,38 @@ on:
             - tests/software/bowtie/**
 
 jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
         env:
-            NXF_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-            - name: Install Nextflow
-              env:
-                  NXF_VER: ${{ matrix.nxf_version }}
-              run: |
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-            - name: Set up Python
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.x"
-            - name: Install dependencies
-              run: python -m pip install --upgrade pip pytest-workflow
+      # Test the module
+      - run: pytest --tag bowtie_align --symlink --wt 2
 
-            # Test the module
-            - run: pytest --tag bowtie_align --symlink --wt 2
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/bowtie_index.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag bowtie_index --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/bwa_index.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag bwa_index --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/bwa_mem.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag bwa_index --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/fastqc.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag fastqc --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/gffread.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag gffread --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/multiqc.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag multiqc --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/picard_collectmultiplemetrics.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/picard_markduplicates.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag picard_markduplicates --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/picard_mergesamfiles.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag picard_mergesamfiles --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/preseq_lcextrap.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag preseq_lcextrap --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/samtools_flagstat.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag samtools_flagstat --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/samtools_idxstats.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag samtools_idxstats --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/samtools_index.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag samtools_index --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/samtools_sort.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag samtools_sort --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/samtools_stats.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag samtools_stats --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/stringtie.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag stringtie --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/trimgalore.yml

@@ -38,3 +38,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag trimgalore --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err

.github/workflows/ucsc_bedgraphtobigwig.yml

@@ -37,3 +37,12 @@ jobs:
 
       # Test the module
       - run: pytest --tag ucsc_bedgraphtobigwig --symlink --wt 2
+
+      - name: Upload logs on failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: |
+            /tmp/pytest_workflow_*/*/log.out
+            /tmp/pytest_workflow_*/*/log.err