From 84b66e4f38301592abd66234b48fe3f0533d05f4 Mon Sep 17 00:00:00 2001 From: sruthipsuresh Date: Thu, 28 Jan 2021 14:38:32 -0600 Subject: [PATCH] Fixed testing, rebased --- .github/filters.yml | 24 ++++++++++++++ .github/workflows/bedtools_complement.yml | 40 ----------------------- .github/workflows/bedtools_genomecov.yml | 40 ----------------------- .github/workflows/bedtools_intersect.yml | 40 ----------------------- .github/workflows/bedtools_merge.yml | 40 ----------------------- .github/workflows/bedtools_slop.yml | 40 ----------------------- .github/workflows/bedtools_sort.yml | 40 ----------------------- 7 files changed, 24 insertions(+), 240 deletions(-) delete mode 100644 .github/workflows/bedtools_complement.yml delete mode 100644 .github/workflows/bedtools_genomecov.yml delete mode 100644 .github/workflows/bedtools_intersect.yml delete mode 100644 .github/workflows/bedtools_merge.yml delete mode 100644 .github/workflows/bedtools_slop.yml delete mode 100644 .github/workflows/bedtools_sort.yml diff --git a/.github/filters.yml b/.github/filters.yml index f8769a2e..73f120d4 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -144,3 +144,27 @@ trimgalore: ucsc_bedgraphtobigwig: - software/ucsc/bedgraphtobigwig/** - tests/software/ucsc/bedgraphtobigwig/** + +bedtools_complement: + - software/bedtools/complement/** + - tests/software/bedtools/** + +bedtools_genomecov: + - software/bedtools/genomecov/** + - tests/software/bedtools/** + +bedtools_intersect: + - software/bedtools/intersect/** + - tests/software/bedtools/** + +bedtools_merge: + - software/bedtools/merge/** + - tests/software/bedtools/** + +bedtools_slop: + - software/bedtools/slop/** + - tests/software/bedtools/** + +bedtools_sort: + - software/bedtools/sort/** + - tests/software/bedtools/** diff --git a/.github/workflows/bedtools_complement.yml b/.github/workflows/bedtools_complement.yml deleted file mode 100644 index e0b27a3c..00000000 --- a/.github/workflows/bedtools_complement.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bedtools_complement -on: - push: - paths: - - software/bedtools/complement/** - - .github/workflows/bedtools_complement.yml - - tests/software/bedtools/** - pull_request: - paths: - - software/bedtools/complement/** - - .github/workflows/bedtools_complement.yml - - tests/software/bedtools/** - -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 bedtools_complement --symlink --wt 2 diff --git a/.github/workflows/bedtools_genomecov.yml b/.github/workflows/bedtools_genomecov.yml deleted file mode 100644 index dc80a464..00000000 --- a/.github/workflows/bedtools_genomecov.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bedtools_genomecov -on: - push: - paths: - - software/bedtools/genomecov/** - - .github/workflows/bedtools_genomecov.yml - - tests/software/bedtools/** - pull_request: - paths: - - software/bedtools/genomecov/** - - .github/workflows/bedtools_genomecov.yml - - tests/software/bedtools/** - -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 bedtools_genomecov --symlink --wt 2 diff --git a/.github/workflows/bedtools_intersect.yml b/.github/workflows/bedtools_intersect.yml deleted file mode 100644 index 3f352dd0..00000000 --- a/.github/workflows/bedtools_intersect.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bedtools_intersect -on: - push: - paths: - - software/bedtools/intersect/** - - .github/workflows/bedtools_intersect.yml - - tests/software/bedtools/** - pull_request: - paths: - - software/bedtools/intersect/** - - .github/workflows/bedtools_intersect.yml - - tests/software/bedtools/** - -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 bedtools_intersect --symlink --wt 2 diff --git a/.github/workflows/bedtools_merge.yml b/.github/workflows/bedtools_merge.yml deleted file mode 100644 index 38ec37df..00000000 --- a/.github/workflows/bedtools_merge.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bedtools_merge -on: - push: - paths: - - software/bedtools/merge/** - - .github/workflows/bedtools_merge.yml - - tests/software/bedtools/** - pull_request: - paths: - - software/bedtools/merge/** - - .github/workflows/bedtools_merge.yml - - tests/software/bedtools/** - -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 bedtools_merge --symlink --wt 2 diff --git a/.github/workflows/bedtools_slop.yml b/.github/workflows/bedtools_slop.yml deleted file mode 100644 index 7cd6f056..00000000 --- a/.github/workflows/bedtools_slop.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bedtools_slop -on: - push: - paths: - - software/bedtools/slop/** - - .github/workflows/bedtools_slop.yml - - tests/software/bedtools/** - pull_request: - paths: - - software/bedtools/slop/** - - .github/workflows/bedtools_slop.yml - - tests/software/bedtools/** - -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 bedtools_slop --symlink --wt 2 diff --git a/.github/workflows/bedtools_sort.yml b/.github/workflows/bedtools_sort.yml deleted file mode 100644 index ee14f308..00000000 --- a/.github/workflows/bedtools_sort.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: bedtools_sort -on: - push: - paths: - - software/bedtools/sort/** - - .github/workflows/bedtools_sort.yml - - tests/software/bedtools/** - pull_request: - paths: - - software/bedtools/sort/** - - .github/workflows/bedtools_sort.yml - - tests/software/bedtools/** - -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 bedtools_sort --symlink --wt 2