From 506ebe515ebf74441c35fa227f036f106762883c Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sat, 23 Jan 2021 23:50:20 -0600 Subject: [PATCH] ci: Move all files to filter file and delete old tests --- .github/filters.yml | 74 ++++++++++++++++++- .github/workflows/bowtie_align.yml | 52 ------------- .github/workflows/bowtie_index.yml | 50 ------------- .github/workflows/bwa_index.yml | 50 ------------- .github/workflows/bwa_mem.yml | 50 ------------- .github/workflows/fastqc.yml | 50 ------------- .github/workflows/gffread.yml | 50 ------------- .github/workflows/multiqc.yml | 50 ------------- .../picard_collectmultiplemetrics.yml | 50 ------------- .github/workflows/picard_markduplicates.yml | 50 ------------- .github/workflows/picard_mergesamfiles.yml | 50 ------------- .github/workflows/preseq_lcextrap.yml | 50 ------------- .github/workflows/samtools_flagstat.yml | 50 ------------- .github/workflows/samtools_idxstats.yml | 50 ------------- .github/workflows/samtools_index.yml | 50 ------------- .github/workflows/samtools_sort.yml | 50 ------------- .github/workflows/samtools_stats.yml | 50 ------------- .github/workflows/stringtie.yml | 50 ------------- .github/workflows/trimgalore.yml | 50 ------------- .github/workflows/ucsc_bedgraphtobigwig.yml | 49 ------------ 20 files changed, 73 insertions(+), 952 deletions(-) delete mode 100644 .github/workflows/bowtie_align.yml delete mode 100644 .github/workflows/bowtie_index.yml delete mode 100644 .github/workflows/bwa_index.yml delete mode 100644 .github/workflows/bwa_mem.yml delete mode 100644 .github/workflows/fastqc.yml delete mode 100644 .github/workflows/gffread.yml delete mode 100644 .github/workflows/multiqc.yml delete mode 100644 .github/workflows/picard_collectmultiplemetrics.yml delete mode 100644 .github/workflows/picard_markduplicates.yml delete mode 100644 .github/workflows/picard_mergesamfiles.yml delete mode 100644 .github/workflows/preseq_lcextrap.yml delete mode 100644 .github/workflows/samtools_flagstat.yml delete mode 100644 .github/workflows/samtools_idxstats.yml delete mode 100644 .github/workflows/samtools_index.yml delete mode 100644 .github/workflows/samtools_sort.yml delete mode 100644 .github/workflows/samtools_stats.yml delete mode 100644 .github/workflows/stringtie.yml delete mode 100644 .github/workflows/trimgalore.yml delete mode 100644 .github/workflows/ucsc_bedgraphtobigwig.yml diff --git a/.github/filters.yml b/.github/filters.yml index d65430e9..03e21d09 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -1,4 +1,76 @@ +bowtie_align: + - software/bowtie/align/** + - software/bowtie/index/** + - tests/software/bowtie/** + +bowtie_index: + - software/bowtie/index/** + - tests/software/bowtie/** + +bwa_index: + - software/bwa/index/** + - tests/software/bwa/** + +bwa_mem: + - software/bwa/mem/** + - tests/software/bwa/** + fastqc: - software/fastqc/** - - .github/workflows/fastqc.yml - tests/software/fastqc/** + +gffread: + - software/gffread/** + - tests/software/gffread/** + +multiqc: + - software/multiqc/** + - tests/software/multiqc/** + +picard_collectmultiplemetrics: + - software/picard/collectmultiplemetrics/** + - tests/software/picard/** + +picard_markduplicates: + - software/picard/markduplicates/** + - tests/software/picard/** + +picard_mergesamfiles: + - software/picard/mergesamfiles/** + - tests/software/picard/** + +preseq_lcextrap: + - software/preseq/lcextrap/** + - tests/software/preseq/** + +samtools_flagstat: + - software/samtools/flagstat/** + - tests/software/samtools/** + +samtools_idxstats: + - software/samtools/idxstats/** + - tests/software/samtools/** + +samtools_index: + - software/samtools/index/** + - tests/software/samtools/** + +samtools_sort: + - software/samtools/sort/** + - tests/software/samtools/** + +samtools_stats: + - software/samtools/stats/** + - tests/software/samtools/** + +stringtie: + - software/stringtie/** + - tests/software/stringtie/** + +trimgalore: + - software/trimgalore/** + - tests/software/trimgalore/** + +ucsc_bedgraphtobigwig: + - software/ucsc/bedgraphtobigwig/** + - tests/software/ucsc/** diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml deleted file mode 100644 index a5ac590c..00000000 --- a/.github/workflows/bowtie_align.yml +++ /dev/null @@ -1,52 +0,0 @@ -name: bowtie_align -on: - push: - paths: - - software/bowtie/align/** - - software/bowtie/index/** - - .github/workflows/bowtie_align.yml - - tests/software/bowtie/** - pull_request: - paths: - - software/bowtie/align/** - - software/bowtie/index/** - - .github/workflows/bowtie_align.yml - - tests/software/bowtie/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_index.yml deleted file mode 100644 index cd1d7501..00000000 --- a/.github/workflows/bowtie_index.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: bowtie_index -on: - push: - paths: - - software/bowtie/index/** - - .github/workflows/bowtie_index.yml - - tests/software/bowtie/** - pull_request: - paths: - - software/bowtie/index/** - - .github/workflows/bowtie_index.yml - - tests/software/bowtie/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/bwa_index.yml b/.github/workflows/bwa_index.yml deleted file mode 100644 index 632dc5be..00000000 --- a/.github/workflows/bwa_index.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: bwa_index -on: - push: - paths: - - software/bwa/index/** - - .github/workflows/software/bwa_index.yml - - tests/software/bwa/** - pull_request: - paths: - - software/bwa/index/** - - .github/workflows/software/bwa_index.yml - - tests/software/bwa/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/bwa_mem.yml b/.github/workflows/bwa_mem.yml deleted file mode 100644 index 2c5ccbcc..00000000 --- a/.github/workflows/bwa_mem.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: bwa_mem -on: - push: - paths: - - software/bwa/mem/** - - .github/workflows/bwa_mem.yml - - tests/software/bwa/** - pull_request: - paths: - - software/bwa/mem/** - - .github/workflows/bwa_mem.yml - - tests/software/bwa/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml deleted file mode 100644 index e9fae495..00000000 --- a/.github/workflows/fastqc.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: fastqc -on: - push: - paths: - - software/fastqc/** - - .github/workflows/fastqc.yml - - tests/software/fastqc/** - pull_request: - paths: - - software/fastqc/** - - .github/workflows/fastqc.yml - - tests/software/fastqc/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --tag fastqc --symlink --wt 2 - - - name: Upload logs on failure - if: ${{ failure() }} - uses: actions/upload-artifact@v2 - with: - name: logs - path: | - /tmp/pytest_workflow_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/gffread.yml b/.github/workflows/gffread.yml deleted file mode 100644 index 01ffa6c2..00000000 --- a/.github/workflows/gffread.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: gffread -on: - push: - paths: - - software/gffread/** - - .github/workflows/gffread.yml - - tests/software/gffread/** - pull_request: - paths: - - software/gffread/** - - .github/workflows/gffread.yml - - tests/software/gffread/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --tag gffread --symlink --wt 2 - - - name: Upload logs on failure - if: ${{ failure() }} - uses: actions/upload-artifact@v2 - with: - name: logs - path: | - /tmp/pytest_workflow_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/multiqc.yml b/.github/workflows/multiqc.yml deleted file mode 100644 index 79d68e94..00000000 --- a/.github/workflows/multiqc.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: multiqc -on: - push: - paths: - - software/multiqc/** - - .github/workflows/multiqc.yml - - tests - pull_request: - paths: - - software/multiqc/** - - .github/workflows/multiqc.yml - - tests - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --tag multiqc --symlink --wt 2 - - - name: Upload logs on failure - if: ${{ failure() }} - uses: actions/upload-artifact@v2 - with: - name: logs - path: | - /tmp/pytest_workflow_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/picard_collectmultiplemetrics.yml b/.github/workflows/picard_collectmultiplemetrics.yml deleted file mode 100644 index 84723c8a..00000000 --- a/.github/workflows/picard_collectmultiplemetrics.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: picard_collectmultiplemetrics -on: - push: - paths: - - software/picard/collectmultiplemetrics/** - - .github/workflows/picard_collectmultiplemetrics.yml - - tests/software/picard/** - pull_request: - paths: - - software/picard/collectmultiplemetrics/** - - .github/workflows/picard_collectmultiplemetrics.yml - - tests/software/picard/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/picard_markduplicates.yml b/.github/workflows/picard_markduplicates.yml deleted file mode 100644 index ff6d7330..00000000 --- a/.github/workflows/picard_markduplicates.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: picard_markduplicates -on: - push: - paths: - - software/picard/markduplicates/** - - .github/workflows/picard_markduplicates.yml - - tests/software/picard/** - pull_request: - paths: - - software/picard/markduplicates/** - - .github/workflows/picard_markduplicates.yml - - tests/software/picard/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/picard_mergesamfiles.yml b/.github/workflows/picard_mergesamfiles.yml deleted file mode 100644 index 92568d10..00000000 --- a/.github/workflows/picard_mergesamfiles.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: picard_mergesamfiles -on: - push: - paths: - - software/picard/mergesamfiles/** - - .github/workflows/picard_mergesamfiles.yml - - tests/software/picard/** - pull_request: - paths: - - software/picard/mergesamfiles/** - - .github/workflows/picard_mergesamfiles.yml - - tests/software/picard/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/preseq_lcextrap.yml b/.github/workflows/preseq_lcextrap.yml deleted file mode 100644 index 5dbb5369..00000000 --- a/.github/workflows/preseq_lcextrap.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: preseq_lcextrap -on: - push: - paths: - - software/preseq/lcextrap/** - - .github/workflows/preseq_lcextrap.yml - - tests/software/preseq/** - pull_request: - paths: - - software/preseq/lcextrap/** - - .github/workflows/preseq_lcextrap.yml - - tests/software/preseq/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_flagstat.yml b/.github/workflows/samtools_flagstat.yml deleted file mode 100644 index 4c9f8396..00000000 --- a/.github/workflows/samtools_flagstat.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: samtools_flagstat -on: - push: - paths: - - software/samtools/flagstat/** - - .github/workflows/samtools_flagstat.yml - - tests/software/samtools/** - pull_request: - paths: - - software/samtools/flagstat/** - - .github/workflows/samtools_flagstat.yml - - tests/software/samtools/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_idxstats.yml b/.github/workflows/samtools_idxstats.yml deleted file mode 100644 index d3f544c7..00000000 --- a/.github/workflows/samtools_idxstats.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: samtools_idxstats -on: - push: - paths: - - software/samtools/idxstats/** - - .github/workflows/samtools_idxstats.yml - - tests/software/samtools/** - pull_request: - paths: - - software/samtools/idxstats/** - - .github/workflows/samtools_idxstats.yml - - tests/software/samtools/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml deleted file mode 100644 index 4bfde947..00000000 --- a/.github/workflows/samtools_index.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: samtools_index -on: - push: - paths: - - software/samtools/index/** - - .github/workflows/samtools_index.yml - - tests/software/samtools/** - pull_request: - paths: - - software/samtools/index/** - - .github/workflows/samtools_index.yml - - tests/software/samtools/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml deleted file mode 100644 index 45e7b563..00000000 --- a/.github/workflows/samtools_sort.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: samtools_sort -on: - push: - paths: - - software/samtools/sort/** - - .github/workflows/samtools_sort.yml - - tests/software/samtools/** - pull_request: - paths: - - software/samtools/sort/** - - .github/workflows/samtools_sort.yml - - tests/software/samtools/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_stats.yml b/.github/workflows/samtools_stats.yml deleted file mode 100644 index e3333d96..00000000 --- a/.github/workflows/samtools_stats.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: samtools_stats -on: - push: - paths: - - software/samtools/stats/** - - .github/workflows/software/samtools_stats.yml - - tests/software/samtools/** - pull_request: - paths: - - software/samtools/stats/** - - .github/workflows/software/samtools_stats.yml - - tests/software/samtools/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/stringtie.yml b/.github/workflows/stringtie.yml deleted file mode 100644 index 6a9606a1..00000000 --- a/.github/workflows/stringtie.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: stringtie -on: - push: - paths: - - software/stringtie/** - - .github/workflows/stringtie.yml - - tests/software/stringtie/** - pull_request: - paths: - - software/stringtie/** - - .github/workflows/stringtie.yml - - tests/software/stringtie/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --tag stringtie --symlink --wt 2 - - - name: Upload logs on failure - if: ${{ failure() }} - uses: actions/upload-artifact@v2 - with: - name: logs - path: | - /tmp/pytest_workflow_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/trimgalore.yml b/.github/workflows/trimgalore.yml deleted file mode 100644 index 392ced96..00000000 --- a/.github/workflows/trimgalore.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: trimgalore -on: - push: - paths: - - software/trimgalore/** - - .github/workflows/trimgalore.yml - - tests/software/trimgalore/** - pull_request: - paths: - - software/trimgalore/** - - .github/workflows/trimgalore.yml - - tests/software/trimgalore/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --tag trimgalore --symlink --wt 2 - - - name: Upload logs on failure - if: ${{ failure() }} - uses: actions/upload-artifact@v2 - with: - name: logs - path: | - /tmp/pytest_workflow_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/ucsc_bedgraphtobigwig.yml b/.github/workflows/ucsc_bedgraphtobigwig.yml deleted file mode 100644 index 300df97c..00000000 --- a/.github/workflows/ucsc_bedgraphtobigwig.yml +++ /dev/null @@ -1,49 +0,0 @@ -name: ucsc_bedgraphtobigwig -on: - push: - paths: - - software/ucsc/bedgraphtobigwig/** - - .github/workflows/ucsc_bedgraphtobigwig.yml - - tests/software/ucsc/** - pull_request: - paths: - - software/ucsc/bedgraphtobigwig/** - - .github/workflows/ucsc_bedgraphtobigwig.yml - - tests/software/ucsc/** - -jobs: - 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_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 - - # Test the module - - run: pytest --kwdof --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_*/*/.nextflow.log - /tmp/pytest_workflow_*/*/log.out - /tmp/pytest_workflow_*/*/log.err