ci: Add keep-workflow-wd-on-fail

.github/workflows/bowtie_align.yml

@@ -39,7 +39,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bowtie_align --symlink --wt 2
+      - run: pytest --kwdof --tag bowtie_align --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/bowtie_index.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bowtie_index --symlink --wt 2
+      - run: pytest --kwdof --tag bowtie_index --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/bwa_index.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bwa_index --symlink --wt 2
+      - run: pytest --kwdof --tag bwa_index --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/bwa_mem.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bwa_index --symlink --wt 2
+      - run: pytest --kwdof --tag bwa_index --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/fastqc.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag fastqc --symlink --wt 2
+      - run: pytest --kwdof --tag fastqc --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/gffread.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag gffread --symlink --wt 2
+      - run: pytest --kwdof --tag gffread --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/multiqc.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag multiqc --symlink --wt 2
+      - run: pytest --kwdof --tag multiqc --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/picard_collectmultiplemetrics.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
+      - run: pytest --kwdof --tag picard_collectmultiplemetrics --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/picard_markduplicates.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag picard_markduplicates --symlink --wt 2
+      - run: pytest --kwdof --tag picard_markduplicates --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/picard_mergesamfiles.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag picard_mergesamfiles --symlink --wt 2
+      - run: pytest --kwdof --tag picard_mergesamfiles --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/preseq_lcextrap.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag preseq_lcextrap --symlink --wt 2
+      - run: pytest --kwdof --tag preseq_lcextrap --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/samtools_flagstat.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag samtools_flagstat --symlink --wt 2
+      - run: pytest --kwdof --tag samtools_flagstat --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/samtools_idxstats.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag samtools_idxstats --symlink --wt 2
+      - run: pytest --kwdof --tag samtools_idxstats --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/samtools_index.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag samtools_index --symlink --wt 2
+      - run: pytest --kwdof --tag samtools_index --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/samtools_sort.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag samtools_sort --symlink --wt 2
+      - run: pytest --kwdof --tag samtools_sort --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/samtools_stats.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag samtools_stats --symlink --wt 2
+      - run: pytest --kwdof --tag samtools_stats --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/stringtie.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag stringtie --symlink --wt 2
+      - run: pytest --kwdof --tag stringtie --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/trimgalore.yml

@@ -37,7 +37,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag trimgalore --symlink --wt 2
+      - run: pytest --kwdof --tag trimgalore --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}

.github/workflows/ucsc_bedgraphtobigwig.yml

@@ -36,7 +36,7 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag ucsc_bedgraphtobigwig --symlink --wt 2
+      - run: pytest --kwdof --tag ucsc_bedgraphtobigwig --symlink --wt 2
 
       - name: Upload logs on failure
         if: ${{ failure() }}