From 73bd2d499e79e1e07e080eab83ff9b1993f0b197 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Jan 2021 11:26:58 -0600 Subject: [PATCH] ci: Add keep-workflow-wd-on-fail --- .github/workflows/bowtie_align.yml | 2 +- .github/workflows/bowtie_index.yml | 2 +- .github/workflows/bwa_index.yml | 2 +- .github/workflows/bwa_mem.yml | 2 +- .github/workflows/fastqc.yml | 2 +- .github/workflows/gffread.yml | 2 +- .github/workflows/multiqc.yml | 2 +- .github/workflows/picard_collectmultiplemetrics.yml | 2 +- .github/workflows/picard_markduplicates.yml | 2 +- .github/workflows/picard_mergesamfiles.yml | 2 +- .github/workflows/preseq_lcextrap.yml | 2 +- .github/workflows/samtools_flagstat.yml | 2 +- .github/workflows/samtools_idxstats.yml | 2 +- .github/workflows/samtools_index.yml | 2 +- .github/workflows/samtools_sort.yml | 2 +- .github/workflows/samtools_stats.yml | 2 +- .github/workflows/stringtie.yml | 2 +- .github/workflows/trimgalore.yml | 2 +- .github/workflows/ucsc_bedgraphtobigwig.yml | 2 +- 19 files changed, 19 insertions(+), 19 deletions(-) diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml index 14222a7b..55c025d7 100644 --- a/.github/workflows/bowtie_align.yml +++ b/.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() }} diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_index.yml index 4fc29026..93ff35df 100644 --- a/.github/workflows/bowtie_index.yml +++ b/.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() }} diff --git a/.github/workflows/bwa_index.yml b/.github/workflows/bwa_index.yml index 5156965d..95395751 100644 --- a/.github/workflows/bwa_index.yml +++ b/.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() }} diff --git a/.github/workflows/bwa_mem.yml b/.github/workflows/bwa_mem.yml index ba3f6609..af5290e5 100644 --- a/.github/workflows/bwa_mem.yml +++ b/.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() }} diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index 59d324ee..504e12ff 100644 --- a/.github/workflows/fastqc.yml +++ b/.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() }} diff --git a/.github/workflows/gffread.yml b/.github/workflows/gffread.yml index 3ff64058..7509eafe 100644 --- a/.github/workflows/gffread.yml +++ b/.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() }} diff --git a/.github/workflows/multiqc.yml b/.github/workflows/multiqc.yml index 8de15621..4070a1df 100644 --- a/.github/workflows/multiqc.yml +++ b/.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() }} diff --git a/.github/workflows/picard_collectmultiplemetrics.yml b/.github/workflows/picard_collectmultiplemetrics.yml index ecccdf70..86130f75 100644 --- a/.github/workflows/picard_collectmultiplemetrics.yml +++ b/.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() }} diff --git a/.github/workflows/picard_markduplicates.yml b/.github/workflows/picard_markduplicates.yml index 02b93a0c..5438d30b 100644 --- a/.github/workflows/picard_markduplicates.yml +++ b/.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() }} diff --git a/.github/workflows/picard_mergesamfiles.yml b/.github/workflows/picard_mergesamfiles.yml index 6aedb733..aa8fa1a4 100644 --- a/.github/workflows/picard_mergesamfiles.yml +++ b/.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() }} diff --git a/.github/workflows/preseq_lcextrap.yml b/.github/workflows/preseq_lcextrap.yml index 997741e1..ea04bc8b 100644 --- a/.github/workflows/preseq_lcextrap.yml +++ b/.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() }} diff --git a/.github/workflows/samtools_flagstat.yml b/.github/workflows/samtools_flagstat.yml index 08106404..3b2a956b 100644 --- a/.github/workflows/samtools_flagstat.yml +++ b/.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() }} diff --git a/.github/workflows/samtools_idxstats.yml b/.github/workflows/samtools_idxstats.yml index ab13eecf..ffd4ce41 100644 --- a/.github/workflows/samtools_idxstats.yml +++ b/.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() }} diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 0dcbd744..74ea3e45 100644 --- a/.github/workflows/samtools_index.yml +++ b/.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() }} diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index 5725ab1a..44b4bc12 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.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() }} diff --git a/.github/workflows/samtools_stats.yml b/.github/workflows/samtools_stats.yml index f71ef4c0..ba346e60 100644 --- a/.github/workflows/samtools_stats.yml +++ b/.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() }} diff --git a/.github/workflows/stringtie.yml b/.github/workflows/stringtie.yml index 80e9b498..d7bb6fff 100644 --- a/.github/workflows/stringtie.yml +++ b/.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() }} diff --git a/.github/workflows/trimgalore.yml b/.github/workflows/trimgalore.yml index c3192afa..5bc54de5 100644 --- a/.github/workflows/trimgalore.yml +++ b/.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() }} diff --git a/.github/workflows/ucsc_bedgraphtobigwig.yml b/.github/workflows/ucsc_bedgraphtobigwig.yml index 8e7a9473..935ad9aa 100644 --- a/.github/workflows/ucsc_bedgraphtobigwig.yml +++ b/.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() }}