ci: Move all files to filter file and delete old tests

.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/**

.github/workflows/bowtie_align.yml

@@ -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

.github/workflows/bowtie_index.yml

@@ -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

.github/workflows/bwa_index.yml

@@ -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

.github/workflows/bwa_mem.yml

@@ -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

.github/workflows/fastqc.yml

@@ -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

.github/workflows/gffread.yml

@@ -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

.github/workflows/multiqc.yml

@@ -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

.github/workflows/picard_collectmultiplemetrics.yml

@@ -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

.github/workflows/picard_markduplicates.yml

@@ -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

.github/workflows/picard_mergesamfiles.yml

@@ -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

.github/workflows/preseq_lcextrap.yml

@@ -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

.github/workflows/samtools_flagstat.yml

@@ -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

.github/workflows/samtools_idxstats.yml

@@ -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

.github/workflows/samtools_index.yml

@@ -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

.github/workflows/samtools_sort.yml

@@ -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

.github/workflows/samtools_stats.yml

@@ -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

.github/workflows/stringtie.yml

@@ -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

.github/workflows/trimgalore.yml

@@ -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

.github/workflows/ucsc_bedgraphtobigwig.yml

@@ -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