ci: Add filters for new modules

These snuck in after the 506ebe5 was written

.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:
+bowtie_build:
-  - software/bowtie/index/**
+  - 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/**

.github/workflows/bowtie2_align.yml

@@ -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

.github/workflows/bowtie2_build.yml

@@ -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

.github/workflows/bowtie_build.yml

@@ -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

.github/workflows/cutadapt.yml

@@ -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

.github/workflows/dsh_filterbed.yml

@@ -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

.github/workflows/dsh_splitbed.yml

@@ -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

.github/workflows/fastp.yml

@@ -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

.github/workflows/pangolin.yml

@@ -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

.github/workflows/quast.yml

@@ -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

.github/workflows/salmon_index.yml

@@ -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

.github/workflows/salmon_quant.yml

@@ -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

.github/workflows/samtools_mpileup.yml

@@ -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

.github/workflows/samtools_view.yml

@@ -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

.github/workflows/seacr_callpeak.yml

@@ -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

.github/workflows/star_align.yml

@@ -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

.github/workflows/star_genomegenerate.yml

@@ -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