ci: Upload logs on failures

.github/workflows/bowtie_align.yml

@@ -40,3 +40,12 @@ jobs:
 
       # 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