Dsl2 variant

.github/workflows/branch.yml

@@ -3,14 +3,35 @@ name: nf-core branch protection
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
   pull_request:
-    branches:
-    - master
+    branches: [master]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
+        if: github.repository == 'nf-core/sarek'
         run: |
-          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/sarek ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            The `master` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+
+            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+

.github/workflows/ci.yml

@@ -32,12 +32,12 @@ jobs:
             environment.yml
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/sarek:dev
+        run: docker build --no-cache . -t nfcore/sarek:dsl2
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dsl2
+          docker tag nfcore/sarek:dsl2 nfcore/sarek:dsl2
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
@@ -46,14 +46,13 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
-  annotation:
+  aligner:
     env:
       NXF_ANSI_LOG: false
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        tools: [snpeff, vep]
-        species: [WBcel235]
+        aligner: [bwa-mem, bwa-mem2]
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow
@@ -64,11 +63,9 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.07.1'
       - name: Pull docker image
-        run: |
-          docker pull nfcore/sarek:dev
-          docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
-      - name: Run annotation test
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}
+        run: docker pull nfcore/sarek:dsl2
+      - name: Run ${{ matrix.profile }} test
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}
 
   germline:
     env:
@@ -87,97 +84,103 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.07.1'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:dsl2
       - name: Get test data
         run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
-      - name: Run germline test
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input data/testdata/tiny/normal --saved_bam_mapped
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step prepare_recalibration -resume
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step recalibrate -resume
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step variantCalling
+      - name: Run germline test --step mapping
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input data/testdata/tiny/normal --save_bam_mapped
+      - name: Run germline test --step prepare_recalibration
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step prepare_recalibration -resume
+      - name: Run germline test --step recalibrate
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step recalibrate -resume
+      - name: Run germline test --step variantCalling
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step variantCalling
 
-  minimal:
-    env:
-      NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        genome: [smallerGRCh37, minimalGRCh37]
-        intervals: [--no_intervals, '']
-    steps:
-      - uses: actions/checkout@v2
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-        env:
-          # Only check Nextflow pipeline minimum version
-          NXF_VER: '20.07.1'
-      - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
-      - name: Run test for minimal genomes
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
+  # annotation:
+  #   env:
+  #     NXF_ANSI_LOG: false
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       tools: [snpeff, vep]
+  #       species: [WBcel235]
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - name: Install Nextflow
+  #       run: |
+  #         wget -qO- get.nextflow.io | bash
+  #         sudo mv nextflow /usr/local/bin/
+  #       env:
+  #         # Only check Nextflow pipeline minimum version
+  #         NXF_VER: '20.07.1'
+  #     - name: Pull docker image
+  #       run: |
+  #         docker pull nfcore/sarek:dsl2
+  #         docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
+  #     - name: Run annotation test
+  #       run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}
 
-  profile:
-    env:
-      NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        profile: [test_split_fastq, test_targeted, test_trimming, test_no_gatk_spark, test_umi_tso, test_umi_qiaseq]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-        env:
-          # Only check Nextflow pipeline minimum version
-          NXF_VER: '20.07.1'
-      - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
-      - name: Run ${{ matrix.profile }} test
-        run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
+  # minimal:
+  #   env:
+  #     NXF_ANSI_LOG: false
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       genome: [smallerGRCh37, minimalGRCh37]
+  #       intervals: [--no_intervals, '']
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - name: Install Nextflow
+  #       run: |
+  #         wget -qO- get.nextflow.io | bash
+  #         sudo mv nextflow /usr/local/bin/
+  #       env:
+  #         # Only check Nextflow pipeline minimum version
+  #         NXF_VER: '20.07.1'
+  #     - name: Pull docker image
+  #       run: docker pull nfcore/sarek:dsl2
+  #     - name: Run test for minimal genomes
+  #       run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
-  aligner:
-    env:
-      NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        aligner: [bwa-mem, bwa-mem2]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-        env:
-          # Only check Nextflow pipeline minimum version
-          NXF_VER: '20.07.1'
-      - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
-      - name: Run ${{ matrix.profile }} test
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}
+  # profile:
+  #   env:
+  #     NXF_ANSI_LOG: false
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       profile: [test_split_fastq, test_targeted, test_trimming, test_no_gatk_spark, test_umi_tso, test_umi_qiaseq]
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - name: Install Nextflow
+  #       run: |
+  #         wget -qO- get.nextflow.io | bash
+  #         sudo mv nextflow /usr/local/bin/
+  #       env:
+  #         # Only check Nextflow pipeline minimum version
+  #         NXF_VER: '20.07.1'
+  #     - name: Pull docker image
+  #       run: docker pull nfcore/sarek:dsl2
+  #     - name: Run ${{ matrix.profile }} test
+  #       run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
 
   tools:
     env:
       NXF_ANSI_LOG: false
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        tool: [Haplotypecaller, Freebayes, Manta, mpileup, MSIsensor, Strelka, TIDDIT]
+        # tool: [Haplotypecaller, Freebayes, Manta, mpileup, MSIsensor, Strelka, TIDDIT]
+        tool: [Haplotypecaller, Strelka]
         intervals: [--no_intervals, '']
         exclude:
-          - tool: Manta
-            intervals: --no_intervals
-          - tool: MSIsensor
-            intervals: --no_intervals
+        #   - tool: Manta
+        #     intervals: --no_intervals
+        #   - tool: MSIsensor
+        #     intervals: --no_intervals
           - tool: Strelka
             intervals: --no_intervals
-          - tool: TIDDIT
-            intervals: --no_intervals
+        #   - tool: TIDDIT
+        #     intervals: --no_intervals
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow
@@ -188,6 +191,6 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.07.1'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:dsl2
       - name: Run ${{ matrix.tool }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}

.github/workflows/linting.yml

@@ -33,18 +33,36 @@ jobs:
   nf-core:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+
       - uses: actions/setup-python@v1
         with:
           python-version: '3.6'
           architecture: 'x64'
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install nf-core
+
       - name: Run nf-core lint
-        run: nf-core lint ${GITHUB_WORKSPACE}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}
+
+      - name: Upload linting log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: linting-log-file
+          path: lint_log.txt
+

Dockerfile

@@ -1,13 +1,17 @@
-FROM nfcore/base:1.9
+FROM nfcore/base:1.10.2
 LABEL authors="Maxime Garcia, Szilveszter Juhos" \
       description="Docker image containing all software requirements for the nf-core/sarek pipeline"
 
 # Install the conda environment
 COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
+RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
 ENV PATH /opt/conda/envs/nf-core-sarek-3.0dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
 RUN conda env export --name nf-core-sarek-3.0dev > nf-core-sarek-3.0dev.yml
+
+# Instruct R processes to use these empty files instead of clashing with a local version
+RUN touch .Rprofile
+RUN touch .Renviron

conf/base.config

@@ -52,7 +52,7 @@ process {
     cache = false
   }
 
-  withName:CONCATVCF {
+  withName:CONCAT_VCF {
     // For unknown reasons, CONCATVCF sometimes fails with SIGPIPE
     // (exit code 141). Rerunning the process will usually work.
     errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}