adding nf-core lint (#31)

* Fix nf-core lint on sarek * Remove extra CI from .travis.yml and GitHub Actions nf-core CI * Add new nf-core extra CI * remove fancy badges * Remove TODO nf-core comments in code * Use 1.1_2 version for rcolorbrewer, according to nf-core lint
nf-core · Sep 4, 2019 · 70fb026 · 70fb026
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diff --git a/.github/workflows/ci-extra.yml b/.github/workflows/ci-extra.yml
@@ -0,0 +1,27 @@
+name: nf-core 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 --test ${{ matrix.test }}
+      - name: Build References
+        run: |
+          ${GITHUB_WORKSPACE}/scripts/build_reference.sh --test ${{ matrix.test }} --verbose --memory 6.GB
+      - name: Run test
+        run: |
+          ${GITHUB_WORKSPACE}/scripts/run_tests.sh --test ${{ matrix.test }} --verbose --memory 6.GB
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -7,7 +7,6 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        test: [ANNOTATESNPEFF, ANNOTATEVEP, GERMLINE, SOMATIC, TARGETED]
         nxf_ver: ['19.04.0', '']
     steps:
       - uses: actions/checkout@v1
@@ -16,12 +15,9 @@ jobs:
           export NXF_VER=${{ matrix.nxf_ver }}
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-      - name: Download image
+      - name: Build references
         run: |
-          ${GITHUB_WORKSPACE}/scripts/download_image.sh -n docker --test ${{ matrix.test }}
-      - name: Build References
-        run: |
-          ${GITHUB_WORKSPACE}/scripts/build_reference.sh --test ${{ matrix.test }} --verbose --memory 6.GB
+          nextflow run ${GITHUB_WORKSPACE}/build.nf -profile test,docker --build --outdir references
       - name: Run test
         run: |
-          ${GITHUB_WORKSPACE}/scripts/run_tests.sh --test ${{ matrix.test }} --verbose --memory 6.GB
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -15,4 +15,26 @@ jobs:
           npm install -g markdownlint-cli
       - name: Run Markdownlint
         run: |
-          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.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}
diff --git a/.travis.yml b/.travis.yml
@@ -2,62 +2,42 @@ sudo: required
 language: python
 jdk: openjdk8
 services: docker
-
-addons:
-  apt:
-    update: true
-
 python: '3.6'
 cache: pip
-
 matrix:
   fast_finish: true
 
-env:
-  matrix:
-    - TEST=ANNOTATEVEP      NXF_VER=19.04.0
-    - TEST=ANNOTATEVEP      NXF_VER=''
-    - TEST=SOMATIC          NXF_VER=19.04.0
-    - TEST=SOMATIC          NXF_VER=''
-    - TEST=TARGETED         NXF_VER=19.04.0
-    - TEST=TARGETED         NXF_VER=''
-    - TEST=GERMLINE         NXF_VER=19.04.0
-    - TEST=GERMLINE         NXF_VER=''
-    - TEST=ANNOTATESNPEFF   NXF_VER=19.04.0
-    - TEST=ANNOTATESNPEFF   NXF_VER=''
-
 before_install:
   # PRs to master are only ok if coming from dev branch
   - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
   # Pull the docker image first so the test doesn't wait for this
-  - "travis_retry ./scripts/download_image.sh -n docker --test $TEST"
+  - 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
 
 install:
   # Install Nextflow
   - mkdir /tmp/nextflow && cd /tmp/nextflow
   - wget -qO- get.nextflow.io | bash
   - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
-  # # Install nf-core/tools
-  # - pip install --upgrade pip
-  # - pip install nf-core
+  # Install nf-core/tools
+  - pip install --upgrade pip
+  - pip install nf-core
   # Reset
   - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
   # Install markdownlint-cli
   - sudo apt-get install npm && npm install -g markdownlint-cli
 
-# Build references if needed
-before_script:
-  - ${TRAVIS_BUILD_DIR}/scripts/build_reference.sh --test $TEST --verbose
+env:
+  - 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
 
-# Actual tests
 script:
-  - "${TRAVIS_BUILD_DIR}/scripts/run_tests.sh --test $TEST --verbose --no-reports"
-
-# Linting
-jobs:
-  include:
-    - stage: "Linting"
-      name: "Markdown"
-      env: TEST=LINT NXF_VER=19.04.0
-      script:
-        - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
+  # Lint the pipeline code
+  - nf-core lint ${TRAVIS_BUILD_DIR}
+  # 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}/build.nf -profile test,docker --build --outdir references
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -43,6 +43,8 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#21](https://github.com/nf-core/sarek/pull/21) - Add tests for latest Nextflow version as well
 - [#21](https://github.com/nf-core/sarek/pull/21) - Add `genomes.config` for genomes without AWS iGenomes
 - [#XXX](https://github.com/nf-core/sarek/pull/XXX) - Use Github actions for CI
+- [#31](https://github.com/nf-core/sarek/pull/31) - Add nf-core lint
+- [#31](https://github.com/nf-core/sarek/pull/31) - Add extra CI to GitHub Actions nf-core extra CI
 
 ### `Changed`
 
@@ -70,13 +72,15 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#18](https://github.com/nf-core/sarek/pull/18), [#29](https://github.com/nf-core/sarek/pull/29) - `--noReports` is now `--skipQC all`
 - [#18](https://github.com/nf-core/sarek/pull/18), [#21](https://github.com/nf-core/sarek/pull/21) - Update logo
 - [#21](https://github.com/nf-core/sarek/pull/21) - Moved smallGRCh37 path to `genomes.config`
+- [#31](https://github.com/nf-core/sarek/pull/31) - Move extra CI to GitHub Actions nf-core extra CI
 
 ### `Removed`
 
 - [#9](https://github.com/nf-core/sarek/pull/9) - Removed `relatedness2` graph from `vcftools stats`
 - [#13](https://github.com/nf-core/sarek/pull/13) - Removed `BamQCmapped` and `BamQCrecalibrated` processes
 - [#13](https://github.com/nf-core/sarek/pull/13) - Removed `CompressVCF`
 - [#18](https://github.com/nf-core/sarek/pull/18) - Removed params `--noReports`
+- [#31](https://github.com/nf-core/sarek/pull/31) - Remove extra CI from Travis CI and GitHub Actions nf-core CI
 
 ### `Fixed`
 
@@ -90,6 +94,8 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#20](https://github.com/nf-core/sarek/pull/20) - Use new logo in README
 - [#20](https://github.com/nf-core/sarek/pull/20) - Fix path to references genomes
 - [#22](https://github.com/nf-core/sarek/pull/22) - Fix --singleCPUMem issue
+- [#31](https://github.com/nf-core/sarek/pull/31) - Fix badges according to nf-core lint
+- [#31](https://github.com/nf-core/sarek/pull/31) - Fix rcolorbrewer version according to nf-core lint
 
 ## [2.3.FIX1] - 2019-03-04
 

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nfcore/base:1.6
+FROM nfcore/base
 LABEL authors="Maxime Garcia" \
       description="Docker image containing all requirements for nf-core/sarek pipeline"