Feature/mergefastq

.github/workflows/code-linting-develop.yml

@@ -0,0 +1,38 @@
+name: Code Linting Develop
+on:
+  pull_request:
+    branches: [develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Install NodeJS
+        uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v2
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)

.github/workflows/nf-core-linting-develop.yml

@@ -0,0 +1,80 @@
+name: nf-core linting develop
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
+on:
+  pull_request:
+    branches: [develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+
+  lint:
+    runs-on: ubuntu-20.04
+    name: ${{ matrix.tags }}
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install nf-core tools
+        run: python -m pip install nf-core
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Lint ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.tags }}
+        # HACK
+        if: startsWith( matrix.tags, 'subworkflow' ) != true
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}

.github/workflows/nf-test-develop.yml

@@ -0,0 +1,177 @@
+name: nf-test-develop
+on:
+  pull_request:
+    branches: [develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/nftest_modules.yml"
+
+  test:
+    runs-on: ubuntu-20.04
+
+    name: ${{ matrix.tags }} ${{ matrix.profile }}
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - profile: "conda"
+            tags: annotsv
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: deepvariant
+          - profile: "conda"
+            tags: ensemblvep/vep
+          - profile: "conda"
+            tags: fastk/fastk
+          - profile: "conda"
+            tags: fastk/histex
+          - profile: "conda"
+            tags: fastk/merge
+          - profile: "conda"
+            tags: fcs/fcsadaptor
+          - profile: "conda"
+            tags: fcs/fcsgx
+          - profile: "conda"
+            tags: gatk4/cnnscorevariants
+          - profile: "conda"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: sentieon/bwaindex
+          - profile: "conda"
+            tags: sentieon/bwamem
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "conda"
+            tags: subworkflows/vcf_annotate_ensemblvep
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tag ${{ matrix.tags }} \
+            --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap