First Release

.circleci/config.yml

@@ -0,0 +1,85 @@
+version: 2.0
+jobs:
+  snpeffgrch37: &buildsnpeff
+    docker:
+      - image: circleci/buildpack-deps:stretch
+    environment:
+      GENOME: GRCh37
+      SNPEFF_CACHE_VERSION: "75"
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          command: docker build -t nfcore/sareksnpeff:2.5.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+      - run:
+          command: |
+            echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+            docker push nfcore/sareksnpeff:2.5.${GENOME}
+
+  snpeffgrch38:
+    << : *buildsnpeff
+    environment:
+      GENOME: GRCh38
+      SNPEFF_CACHE_VERSION: "86"
+
+  snpeffgrcm38:
+    << : *buildsnpeff
+    environment:
+      GENOME: GRCm38
+      SNPEFF_CACHE_VERSION: "86"
+
+  snpeffcanfam3_1:
+    << : *buildsnpeff
+    environment:
+      GENOME: CanFam3.1
+      SNPEFF_CACHE_VERSION: "86"
+
+  vepgrch37: &buildvep
+    docker:
+      - image: circleci/buildpack-deps:stretch
+    environment:
+      GENOME: GRCh37
+      SPECIES: homo_sapiens
+      VEP_VERSION: "95"
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          command: docker build -t nfcore/sarekvep:2.5.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          no_output_timeout: 3h
+      - run:
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:2.5.${GENOME}
+
+  vepgrch38:
+    << : *buildvep
+    environment:
+      GENOME: GRCh38
+      SPECIES: homo_sapiens
+      VEP_VERSION: "95"
+
+  vepgrcm38:
+    << : *buildvep
+    environment:
+      GENOME: GRCm38
+      SPECIES: mus_musculus
+      VEP_VERSION: "95"
+
+  vepcanfam3_1:
+    << : *buildvep
+    environment:
+      GENOME: CanFam3.1
+      SPECIES: canis_familiaris
+      VEP_VERSION: "95"
+
+workflows:
+  version: 2
+  build:
+    jobs:
+      - snpeffcanfam3_1
+      - snpeffgrch37
+      - snpeffgrch38
+      - snpeffgrcm38
+      - vepcanfam3_1
+      - vepgrch37
+      - vepgrch38
+      - vepgrcm38

.github/CONTRIBUTING.md

@@ -44,4 +44,4 @@ If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.
 
 ## Getting help
-For further information/help, please consult the [nf-core/sarek documentation](https://github.com/nf-core/sarek#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+For further information/help, please consult the [nf-core/sarek documentation](https://github.com/nf-core/sarek#documentation) and don't hesitate to get in touch on the [sarek pipeline channel](https://nfcore.slack.com/channels/sarek) on [Slack](https://nf-co.re/join/slack).

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,15 +1,16 @@
 Many thanks to contributing to nf-core/sarek!
 
-Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
 
 ## PR checklist
  - [ ] This comment contains a description of changes (with reason)
  - [ ] If you've fixed a bug or added code that should be tested, add tests!
- - [ ] If necessary, also make a PR on the [nf-core/sarek branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/sarek)
+ - [ ] If necessary, also make a PR on the [nf-core/sarek branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/sarek)
  - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
  - [ ] Make sure your code lints (`nf-core lint .`).
  - [ ] Documentation in `docs` is updated
  - [ ] `CHANGELOG.md` is updated
  - [ ] `README.md` is updated
 
-**Learn more about contributing:** https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md
+**Learn more about contributing:** [guidelines](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)

.github/markdownlint.yml

@@ -7,3 +7,6 @@ blanks-around-lists: false
 header-increment: false
 no-duplicate-header:
     siblings_only: true
+no-inline-html: 
+    allowed_elements:
+        - img

.github/workflows/branch.yml

@@ -0,0 +1,16 @@
+name: sarek branch protection
+# This workflow is triggered on PRs to master branch on the repository
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      # PRs are only ok if coming from an nf-core dev branch
+      - uses: actions/checkout@v1
+      - name: Check PRs
+        run: |
+          [[ $(git remote get-url origin) == *nf-core/sarek ]] && [ ${GITHUB_BASE_REF} = "master" ] && [ ${GITHUB_HEAD_REF} = "dev" ]

.github/workflows/ci-extra.yml

@@ -0,0 +1,24 @@
+name: sarek extra CI
+# This workflow is triggered on pushes and PRs to the repository.
+on: [push, pull_request]  
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        test: [ANNOTATESNPEFF, ANNOTATEVEP, GERMLINE, SOMATIC, TARGETED]
+        nxf_ver: ['19.04.0', '']
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          export NXF_VER=${{ matrix.nxf_ver }}
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Download image
+        run: |
+          ${GITHUB_WORKSPACE}/scripts/download_image.sh -n docker --source-version dev --target-version 2.5 --test ${{ matrix.test }}
+      - name: Run test
+        run: |
+          ${GITHUB_WORKSPACE}/scripts/run_tests.sh --test ${{ matrix.test }} --verbose

.github/workflows/ci.yml

@@ -0,0 +1,24 @@
+name: sarek CI
+# This workflow is triggered on pushes and PRs to the repository.
+on: [push, pull_request]  
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_ver: ['19.04.0', '']
+    steps:
+      - uses: actions/checkout@v1
+      - 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
+        run: |
+          docker pull nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:2.5
+      - name: Run test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker

.github/workflows/linting.yml

@@ -0,0 +1,53 @@
+name: sarek linting
+# This workflow is triggered on pushes and PRs to the repository.
+on: [push, pull_request]  
+
+jobs:
+  Markdown:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+      - name: Install markdownlint
+        run: |
+          npm install -g markdownlint-cli
+      - name: Run Markdownlint
+        run: |
+          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+  YAML:
+    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")
+  nf-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - 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 pip
+        run: |
+          sudo apt install python3-pip
+          pip install --upgrade pip
+      - name: Install nf-core tools
+        run: |
+          pip install nf-core
+      - name: Run nf-core lint
+        run: |
+          nf-core lint ${GITHUB_WORKSPACE}

.gitignore

@@ -1,6 +1,7 @@
 .nextflow*
 work/
 data/
+references/
 results/
 .DS_Store
 tests/test_data

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/sarek:dev
   # Fake the tag locally so that the pipeline runs properly
   # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/sarek:dev nfcore/sarek:dev
+  - docker tag nfcore/sarek:dev nfcore/sarek:2.5
 
 install:
   # Install Nextflow
@@ -30,7 +30,7 @@ install:
   - sudo apt-get install npm && npm install -g markdownlint-cli
 
 env:
-  - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='19.04.0' # Specify a minimum NF version that should be tested and work
   - NXF_VER='' # Plus: get the latest NF version and check that it works
 
 script:
@@ -39,4 +39,4 @@ script:
   # Lint the documentation
   - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
   # Run the pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker