Merge branch 'TEMPLATE' into dev

nf-core · Feb 26, 2020 · 829875d · 829875d
2 parents 8972a6c + 309b7ce
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -35,7 +35,7 @@ A clear and concise description of what you expected to happen.
 
 - Engine: <!-- [e.g. Conda, Docker or Singularity] -->
 - version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. nfcore/sarek:2.5.1] -->
+- Image tag: <!-- [e.g. nfcore/sarek:2.5.2] -->
 
 ## Additional context
 

diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml
@@ -1,10 +1,6 @@
 # Markdownlint configuration file
 default: true,
 line-length: false
-no-multiple-blanks: 0
-blanks-around-headers: false
-blanks-around-lists: false
-header-increment: false
 no-duplicate-header:
     siblings_only: true
 no-inline-html: 

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -1,15 +1,16 @@
-name: sarek branch protection
-# This workflow is triggered on PRs to master branch on the repository
+name: nf-core branch protection
+# This workflow is triggered on PRs to `master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
   pull_request:
     branches:
     - master
 
 jobs:
   test:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
       - name: Check PRs
         run: |
-          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
+          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,61 +1,74 @@
-name: sarek CI
+name: nf-core CI
 # This workflow is triggered on pushes and PRs to the repository.
-on: [push, pull_request]  
+# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors.
+on: [push, pull_request]
 
 jobs:
   test:
-    runs-on: ubuntu-18.04
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
     strategy:
       matrix:
+        # Nextflow versions: check pipeline minimum and current latest
         nxf_ver: ['19.10.0', '']
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - name: Install Nextflow
         run: |
-          export NXF_VER=${{ matrix.nxf_ver }}
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-      - name: Download and tag image
+      - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+
   annotation:
-    runs-on: ubuntu-18.04
+    env:
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         tools: [snpeff]
         species: [GRCh37]
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
         env:
+          # Only check Nextflow pipeline minimum version for other C
           NXF_VER: '19.10.0'
-      - name: Download and tag images
+      - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
           docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
           docker tag nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }} nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
       - name: Run annotation test
-        run: |
-          nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.tools }}
+        run: nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.tools }}
+
   germline:
-    runs-on: ubuntu-18.04
+    env:
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - 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 for other C
           NXF_VER: '19.10.0'
-      - name: Download and tag image
+      - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Get test data
         run: |
           git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
@@ -64,61 +77,73 @@ jobs:
           nextflow run . -profile test,docker --input data/testdata/tiny/normal
           nextflow run . -profile test,docker --input=false --step recalibrate -resume
           nextflow run . -profile test,docker --input=false --step variantCalling
+
   minimal:
-    runs-on: ubuntu-18.04
+    env:
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         genome: [smallerGRCh37, minimalGRCh37]
         intervals: [--no_intervals, '']
     steps:
-      - uses: actions/checkout@v1
+      - 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 for other C
           NXF_VER: '19.10.0'
-      - name: Download and tag image
+      - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test for minimal genomes
-        run: |
-          nextflow run . -profile test,docker --skipQC all --verbose --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka
+        run: nextflow run . -profile test,docker --skipQC all --verbose --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka
+
   profile:
-    runs-on: ubuntu-18.04
+    env:
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        profile: [test_splitfastq, test_targeted]
+        profile: [test_splitfastq, test_targeted, test_trimming]
     steps:
-      - uses: actions/checkout@v1
+      - 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 for other C
           NXF_VER: '19.10.0'
-      - name: Download and tag image
+      - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run ${{ matrix.profile }} test
-        run: |
-          nextflow run . -profile ${{ matrix.profile }},docker --verbose
+        run: nextflow run . -profile ${{ matrix.profile }},docker --verbose
+
   tools:
-    runs-on: ubuntu-18.04
+    env:
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         tool: [Haplotypecaller, Freebayes, Manta, mpileup, Strelka, TIDDIT]
     steps:
-      - uses: actions/checkout@v1
+      - 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 for other C
           NXF_VER: '19.10.0'
-      - name: Download and tag image
+      - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run ${{ matrix.tool }} test
-        run: |
-          nextflow run . -profile test_tool,docker --verbose --tools ${{ matrix.tool }}
+        run: nextflow run . -profile test_tool,docker --verbose --tools ${{ matrix.tool }}
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -1,38 +1,39 @@
-name: sarek linting
+name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-on: [push, pull_request]  
+# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
 
 jobs:
   Markdown:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - uses: actions/setup-node@v1
         with:
           node-version: '10'
       - name: Install markdownlint
-        run: |
-          npm install -g markdownlint-cli
+        run: npm install -g markdownlint-cli
       - name: Run Markdownlint
-        run: |
-          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
   YAML:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
       - uses: actions/setup-node@v1
         with:
           node-version: '10'
-      - name: Install yamllint
-        run: |
-          npm install -g yaml-lint
-      - name: Run yamllint
-        run: |
-          yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
+      - name: Install yaml-lint
+        run: npm install -g yaml-lint
+      - name: Run yaml-lint
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
   nf-core:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
@@ -41,13 +42,9 @@ jobs:
         with:
           python-version: '3.6'
           architecture: 'x64'
-      - name: Install pip
+      - name: Install dependencies
         run: |
-          sudo apt install python3-pip
-          pip install --upgrade pip
-      - name: Install nf-core tools
-        run: |
-          pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+          python -m pip install --upgrade pip
+          pip install nf-core
       - name: Run nf-core lint
-        run: |
-          nf-core lint ${GITHUB_WORKSPACE}
+        run: nf-core lint ${GITHUB_WORKSPACE}
diff --git a/.gitignore b/.gitignore
@@ -4,5 +4,6 @@ data/
 references/
 results/
 .DS_Store
-tests/test_data
+tests/
+testing/
 *.pyc
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 ## dev
 
 ### `Added`
+
 - [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
 - [#76](https://github.com/nf-core/sarek/pull/76) - Add `GATK Spark` possibilities to Sarek
 - [#87](https://github.com/nf-core/sarek/pull/87) - Add `GATK BaseRecalibrator` plot to `MultiQC` report
@@ -22,12 +23,17 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#107](https://github.com/nf-core/sarek/pull/107) - Switch params to snake_case
 - [#109](https://github.com/nf-core/sarek/pull/109) - Update publication with F1000Research preprint
 - [#113](https://github.com/nf-core/sarek/pull/113) - Move social preview image
+- [#120](https://github.com/nf-core/sarek/pull/120) - Sync TEMPLATE
+- [#121](https://github.com/nf-core/sarek/pull/121) - Update `MultiQC` to `1.8`
+- [#126](https://github.com/nf-core/sarek/pull/126) - Update docs
 
 ### `Fixed`
 
 - [#83](https://github.com/nf-core/sarek/pull/83) - Fix some typos in `docs/input.md`
 - [#107](https://github.com/nf-core/sarek/pull/107) - Fix linting
 - [#110](https://github.com/nf-core/sarek/pull/110) - Fix `snpEff` report issue cf [#106](https://github.com/nf-core/sarek/issues/106)
+- [#126](https://github.com/nf-core/sarek/pull/126) - Fix `iGenomes` paths
+- [#127](https://github.com/nf-core/sarek/pull/127), [#128](https://github.com/nf-core/sarek/pull/128) - Fix `ASCAT`
 
 ### `Deprecated`
 

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-core-invite.herokuapp.com/). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 

diff --git a/Dockerfile b/Dockerfile
@@ -1,8 +1,13 @@
-FROM nfcore/base:dev
+FROM nfcore/base:1.9
 LABEL authors="Maxime Garcia, Szilveszter Juhos" \
-      description="Docker image containing all requirements for nf-core/sarek pipeline"
+      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
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-sarek-dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
 RUN conda env export --name nf-core-sarek-dev > nf-core-sarek-dev.yml
-ENV PATH /opt/conda/envs/nf-core-sarek-dev/bin:$PATH