mirror of
https://github.com/MillironX/nf-core_modules.git
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ci: Upload logs on failures
This commit is contained in:
parent
daa25b9329
commit
a1f4d53d3e
19 changed files with 193 additions and 22 deletions
9
.github/workflows/bowtie_align.yml
vendored
9
.github/workflows/bowtie_align.yml
vendored
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@ -40,3 +40,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag bowtie_align --symlink --wt 2
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- run: pytest --tag bowtie_align --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/bowtie_index.yml
vendored
9
.github/workflows/bowtie_index.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag bowtie_index --symlink --wt 2
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- run: pytest --tag bowtie_index --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/bwa_index.yml
vendored
9
.github/workflows/bwa_index.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag bwa_index --symlink --wt 2
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- run: pytest --tag bwa_index --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/bwa_mem.yml
vendored
9
.github/workflows/bwa_mem.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag bwa_index --symlink --wt 2
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- run: pytest --tag bwa_index --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/fastqc.yml
vendored
9
.github/workflows/fastqc.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag fastqc --symlink --wt 2
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- run: pytest --tag fastqc --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/gffread.yml
vendored
9
.github/workflows/gffread.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag gffread --symlink --wt 2
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- run: pytest --tag gffread --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/multiqc.yml
vendored
9
.github/workflows/multiqc.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag multiqc --symlink --wt 2
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- run: pytest --tag multiqc --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
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- run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/picard_markduplicates.yml
vendored
9
.github/workflows/picard_markduplicates.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag picard_markduplicates --symlink --wt 2
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- run: pytest --tag picard_markduplicates --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/picard_mergesamfiles.yml
vendored
9
.github/workflows/picard_mergesamfiles.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag picard_mergesamfiles --symlink --wt 2
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- run: pytest --tag picard_mergesamfiles --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/preseq_lcextrap.yml
vendored
9
.github/workflows/preseq_lcextrap.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag preseq_lcextrap --symlink --wt 2
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- run: pytest --tag preseq_lcextrap --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/samtools_flagstat.yml
vendored
9
.github/workflows/samtools_flagstat.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag samtools_flagstat --symlink --wt 2
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- run: pytest --tag samtools_flagstat --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/samtools_idxstats.yml
vendored
9
.github/workflows/samtools_idxstats.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag samtools_idxstats --symlink --wt 2
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- run: pytest --tag samtools_idxstats --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/samtools_index.yml
vendored
9
.github/workflows/samtools_index.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag samtools_index --symlink --wt 2
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- run: pytest --tag samtools_index --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/samtools_sort.yml
vendored
9
.github/workflows/samtools_sort.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag samtools_sort --symlink --wt 2
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- run: pytest --tag samtools_sort --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/samtools_stats.yml
vendored
9
.github/workflows/samtools_stats.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag samtools_stats --symlink --wt 2
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- run: pytest --tag samtools_stats --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/stringtie.yml
vendored
9
.github/workflows/stringtie.yml
vendored
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag stringtie --symlink --wt 2
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- run: pytest --tag stringtie --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/trimgalore.yml
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9
.github/workflows/trimgalore.yml
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@ -38,3 +38,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag trimgalore --symlink --wt 2
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- run: pytest --tag trimgalore --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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9
.github/workflows/ucsc_bedgraphtobigwig.yml
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9
.github/workflows/ucsc_bedgraphtobigwig.yml
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@ -37,3 +37,12 @@ jobs:
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# Test the module
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# Test the module
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- run: pytest --tag ucsc_bedgraphtobigwig --symlink --wt 2
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- run: pytest --tag ucsc_bedgraphtobigwig --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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