From 35ac5c5f1504b697a9ee3ae5cae730bcc14ec1bb Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 2 Feb 2021 15:27:45 -0600 Subject: [PATCH] ci: Add filters for new modules These snuck in after the 506ebe5 was written --- .github/filters.yml | 68 ++++++++++++++++++++++- .github/workflows/bowtie2_align.yml | 42 -------------- .github/workflows/bowtie2_build.yml | 40 ------------- .github/workflows/bowtie_build.yml | 40 ------------- .github/workflows/cutadapt.yml | 40 ------------- .github/workflows/dsh_filterbed.yml | 40 ------------- .github/workflows/dsh_splitbed.yml | 40 ------------- .github/workflows/fastp.yml | 40 ------------- .github/workflows/pangolin.yml | 40 ------------- .github/workflows/quast.yml | 40 ------------- .github/workflows/salmon_index.yml | 40 ------------- .github/workflows/salmon_quant.yml | 40 ------------- .github/workflows/samtools_mpileup.yml | 40 ------------- .github/workflows/samtools_view.yml | 40 ------------- .github/workflows/seacr_callpeak.yml | 40 ------------- .github/workflows/star_align.yml | 40 ------------- .github/workflows/star_genomegenerate.yml | 40 ------------- 17 files changed, 65 insertions(+), 645 deletions(-) delete mode 100644 .github/workflows/bowtie2_align.yml delete mode 100644 .github/workflows/bowtie2_build.yml delete mode 100644 .github/workflows/bowtie_build.yml delete mode 100644 .github/workflows/cutadapt.yml delete mode 100644 .github/workflows/dsh_filterbed.yml delete mode 100644 .github/workflows/dsh_splitbed.yml delete mode 100644 .github/workflows/fastp.yml delete mode 100644 .github/workflows/pangolin.yml delete mode 100644 .github/workflows/quast.yml delete mode 100644 .github/workflows/salmon_index.yml delete mode 100644 .github/workflows/salmon_quant.yml delete mode 100644 .github/workflows/samtools_mpileup.yml delete mode 100644 .github/workflows/samtools_view.yml delete mode 100644 .github/workflows/seacr_callpeak.yml delete mode 100644 .github/workflows/star_align.yml delete mode 100644 .github/workflows/star_genomegenerate.yml diff --git a/.github/filters.yml b/.github/filters.yml index 03e21d09..73f4637a 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -1,10 +1,19 @@ +bowtie2_align: + - software/bowtie2/align/** + - software/bowtie2/build/** + - tests/software/bowtie2/** + +bowtie2_build: + - software/bowtie2/build/** + - tests/software/bowtie2/** + bowtie_align: - software/bowtie/align/** - - software/bowtie/index/** + - software/bowtie/build/** - tests/software/bowtie/** -bowtie_index: - - software/bowtie/index/** +bowtie_build: + - software/bowtie/build/** - tests/software/bowtie/** bwa_index: @@ -15,6 +24,22 @@ bwa_mem: - software/bwa/mem/** - tests/software/bwa/** +cutadapt: + - software/cutadapt/** + - tests/software/cutadapt/** + +dsh_filterbed: + - software/dsh/filterbed/** + - tests/software/dsh/** + +dsh_splitbed: + - software/dsh/splitbed/** + - tests/software/dsh/** + +fastp: + - software/fastp/** + - tests/software/fastp/** + fastqc: - software/fastqc/** - tests/software/fastqc/** @@ -27,6 +52,10 @@ multiqc: - software/multiqc/** - tests/software/multiqc/** +pangolin: + - software/pangolin/** + - tests/software/pangolin/** + picard_collectmultiplemetrics: - software/picard/collectmultiplemetrics/** - tests/software/picard/** @@ -43,6 +72,18 @@ preseq_lcextrap: - software/preseq/lcextrap/** - tests/software/preseq/** +quast: + - software/quast/** + - tests/software/quast/** + +salmon_index: + - software/salmon/index/** + - tests/software/salmon/** + +salmon_quant: + - software/salmon/quant/** + - tests/software/salmon/** + samtools_flagstat: - software/samtools/flagstat/** - tests/software/samtools/** @@ -55,6 +96,10 @@ samtools_index: - software/samtools/index/** - tests/software/samtools/** +samtools_mpileup: + - software/samtools/mpileup/** + - tests/software/samtools/** + samtools_sort: - software/samtools/sort/** - tests/software/samtools/** @@ -63,6 +108,23 @@ samtools_stats: - software/samtools/stats/** - tests/software/samtools/** +samtools_view: + - software/samtools/view/** + - tests/software/samtools/** + +seacr_callpeak: + - software/seacr/callpeak/** + - tests/software/seacr/** + +star_align: + - software/star/align/** + - tests/software/star/** + +star_genomegenerate: + - software/star/genomegenerate/** + - tests/software/star/** + + stringtie: - software/stringtie/** - tests/software/stringtie/** diff --git a/.github/workflows/bowtie2_align.yml b/.github/workflows/bowtie2_align.yml deleted file mode 100644 index 3642b5c9..00000000 --- a/.github/workflows/bowtie2_align.yml +++ /dev/null @@ -1,42 +0,0 @@ -name: bowtie2_align -on: - push: - paths: - - software/bowtie2/align/** - - software/bowtie2/build/** - - .github/workflows/bowtie2_align.yml - - tests/software/bowtie2/** - pull_request: - paths: - - software/bowtie2/align/** - - software/bowtie2/build/** - - .github/workflows/bowtie2_align.yml - - tests/software/bowtie2/** - -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 --tag bowtie2_align --symlink --wt 2 diff --git a/.github/workflows/bowtie2_build.yml b/.github/workflows/bowtie2_build.yml deleted file mode 100644 index 21ddde78..00000000 --- a/.github/workflows/bowtie2_build.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bowtie2_build -on: - push: - paths: - - software/bowtie2/build/** - - .github/workflows/bowtie2_build.yml - - tests/software/bowtie2/** - pull_request: - paths: - - software/bowtie2/build/** - - .github/workflows/bowtie2_build.yml - - tests/software/bowtie2/** - -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 --tag bowtie2_build --symlink --wt 2 diff --git a/.github/workflows/bowtie_build.yml b/.github/workflows/bowtie_build.yml deleted file mode 100644 index 1a02341e..00000000 --- a/.github/workflows/bowtie_build.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bowtie_build -on: - push: - paths: - - software/bowtie/build/** - - .github/workflows/bowtie_build.yml - - tests/software/bowtie/** - pull_request: - paths: - - software/bowtie/build/** - - .github/workflows/bowtie_build.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 --tag bowtie_build --symlink --wt 2 diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/cutadapt.yml deleted file mode 100644 index 22bc5171..00000000 --- a/.github/workflows/cutadapt.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: cutadapt -on: - push: - paths: - - software/cutadapt/** - - .github/workflows/cutadapt.yml - - tests/software/cutadapt/** - pull_request: - paths: - - software/cutadapt/** - - .github/workflows/cutadapt.yml - - tests/software/cutadapt/** - -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 --tag cutadapt --symlink --wt 2 diff --git a/.github/workflows/dsh_filterbed.yml b/.github/workflows/dsh_filterbed.yml deleted file mode 100644 index 1d99dbb8..00000000 --- a/.github/workflows/dsh_filterbed.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: dsh_filterbed -on: - push: - paths: - - software/dsh/filterbed/** - - .github/workflows/dsh_filterbed.yml - - tests/software/dsh/** - pull_request: - paths: - - software/dsh/filterbed/** - - .github/workflows/dsh_filterbed.yml - - tests/software/dsh/** - -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 --tag dsh_filterbed --symlink --wt 2 diff --git a/.github/workflows/dsh_splitbed.yml b/.github/workflows/dsh_splitbed.yml deleted file mode 100644 index f2ebbd88..00000000 --- a/.github/workflows/dsh_splitbed.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: dsh_splitbed -on: - push: - paths: - - software/dsh/splitbed/** - - .github/workflows/dsh_splitbed.yml - - tests/software/dsh/** - pull_request: - paths: - - software/dsh/splitbed/** - - .github/workflows/dsh_splitbed.yml - - tests/software/dsh/** - -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 --tag dsh_splitbed --symlink --wt 2 diff --git a/.github/workflows/fastp.yml b/.github/workflows/fastp.yml deleted file mode 100644 index 90ad15ef..00000000 --- a/.github/workflows/fastp.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: fastp -on: - push: - paths: - - software/fastp/** - - .github/workflows/fastp.yml - - tests - pull_request: - paths: - - software/fastp/** - - .github/workflows/fastp.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 --tag fastp --symlink --wt 2 diff --git a/.github/workflows/pangolin.yml b/.github/workflows/pangolin.yml deleted file mode 100644 index 44d718f7..00000000 --- a/.github/workflows/pangolin.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: pangolin -on: - push: - paths: - - software/pangolin/** - - .github/workflows/pangolin.yml - - tests - pull_request: - paths: - - software/pangolin/** - - .github/workflows/pangolin.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 --tag pangolin --symlink --wt 2 diff --git a/.github/workflows/quast.yml b/.github/workflows/quast.yml deleted file mode 100644 index 669d916b..00000000 --- a/.github/workflows/quast.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: quast -on: - push: - paths: - - software/quast/** - - .github/workflows/quast.yml - - tests - pull_request: - paths: - - software/pquast/** - - .github/workflows/quest.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 --tag quast --symlink --wt 2 diff --git a/.github/workflows/salmon_index.yml b/.github/workflows/salmon_index.yml deleted file mode 100644 index e3b065e8..00000000 --- a/.github/workflows/salmon_index.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: salmon_index -on: - push: - paths: - - software/salmon/index/** - - .github/workflows/salmon_index.yml - - tests/software/salmon/** - pull_request: - paths: - - software/salmon/index/** - - .github/workflows/salmon_index.yml - - tests/software/salmon/** - -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 --tag salmon_index --symlink --wt 2 diff --git a/.github/workflows/salmon_quant.yml b/.github/workflows/salmon_quant.yml deleted file mode 100644 index 16a6bf9c..00000000 --- a/.github/workflows/salmon_quant.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: salmon_quant -on: - push: - paths: - - software/salmon/quant/** - - .github/workflows/salmon_quant.yml - - tests/software/salmon/** - pull_request: - paths: - - software/salmon/quant/** - - .github/workflows/salmon_quant.yml - - tests/software/salmon/** - -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 --tag salmon_quant --symlink --wt 2 diff --git a/.github/workflows/samtools_mpileup.yml b/.github/workflows/samtools_mpileup.yml deleted file mode 100644 index 76d92996..00000000 --- a/.github/workflows/samtools_mpileup.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: samtools_mpileup -on: - push: - paths: - - software/samtools/mpileup/** - - .github/workflows/samtools_mpileup.yml - - tests/software/samtools/** - pull_request: - paths: - - software/samtools/mpileup/** - - .github/workflows/samtools_mpileup.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 --tag samtools_mpileup --symlink --wt 2 diff --git a/.github/workflows/samtools_view.yml b/.github/workflows/samtools_view.yml deleted file mode 100644 index a73ef9e3..00000000 --- a/.github/workflows/samtools_view.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: samtools_view -on: - push: - paths: - - software/samtools/view/** - - .github/workflows/samtools_view.yml - - tests/software/samtools/** - pull_request: - paths: - - software/samtools/view/** - - .github/workflows/samtools_view.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 --tag samtools_view --symlink --wt 2 diff --git a/.github/workflows/seacr_callpeak.yml b/.github/workflows/seacr_callpeak.yml deleted file mode 100644 index 3d73a43e..00000000 --- a/.github/workflows/seacr_callpeak.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: seacr_callpeak -on: - push: - paths: - - software/seacr/callpeak/** - - .github/workflows/seacr_callpeak.yml - - tests/software/seacr/** - pull_request: - paths: - - software/seacr/callpeak/** - - .github/workflows/seacr_callpeak.yml - - tests/software/seacr/** - -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 --tag seacr_callpeak --symlink --wt 2 diff --git a/.github/workflows/star_align.yml b/.github/workflows/star_align.yml deleted file mode 100644 index 76dd333d..00000000 --- a/.github/workflows/star_align.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: star_genomegenerate -on: - push: - paths: - - software/star/align/** - - .github/workflows/star_align.yml - - tests/software/star/** - pull_request: - paths: - - software/star/align/** - - .github/workflows/star_align.yml - - tests/software/star/** - -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 --tag star_align --symlink --wt 2 diff --git a/.github/workflows/star_genomegenerate.yml b/.github/workflows/star_genomegenerate.yml deleted file mode 100644 index dcd3884e..00000000 --- a/.github/workflows/star_genomegenerate.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: star_genomegenerate -on: - push: - paths: - - software/star/genomegenerate/** - - .github/workflows/star_genomegenerate.yml - - tests/software/star/** - pull_request: - paths: - - software/star/genomegenerate/** - - .github/workflows/star_genomegenerate.yml - - tests/software/star/** - -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 --tag star_genomegenerate --symlink --wt 2