Add GitHubActions

.github/workflows/ci.yml

@@ -0,0 +1,27 @@
+name: nf-core/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:
+        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

.github/workflows/linting.yml

@@ -0,0 +1,18 @@
+name: nf-core/sarek lint
+# 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

.travis.yml

@@ -58,6 +58,6 @@ jobs:
   include:
     - stage: "Linting"
       name: "Markdown"
-      env: TEST=GERMLINE NXF_VER=19.04.0
+      env: TEST=LINT NXF_VER=19.04.0
       script:
         - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml

CHANGELOG.md

@@ -42,6 +42,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#20](https://github.com/nf-core/sarek/pull/20) - Add `markdownlint` config file
 - [#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
 
 ### `Changed`
 

scripts/build_reference.sh

@@ -4,14 +4,15 @@ set -xeuo pipefail
 # This script build small reference for sarek tests
 # https://github.com/nf-core/test-datasets/raw/sarek
 
-usage() { echo "Usage: $0 <-p profile> <-t test> <-v>" 1>&2; exit 1; }
+usage() { echo "Usage: $0 <-p profile> <-t test> <-v> <-m memory>" 1>&2; exit 1; }
 
+MEMORY='7.GB'
 NXF_SINGULARITY_CACHEDIR=${NXF_SINGULARITY_CACHEDIR:-work/singularity/.}
 OFFLINE=''
 PROFILE=docker
 TEST=ALL
-TRAVIS_BUILD_DIR=${TRAVIS_BUILD_DIR:-.}
 TRAVIS=${TRAVIS:-false}
+TRAVIS_BUILD_DIR=${TRAVIS_BUILD_DIR:-.}
 VERBOSE=''
 
 while [[ $# -gt 0 ]]
@@ -23,6 +24,11 @@ do
     shift # past argument
     shift # past value
     ;;
+    -m|--memory)
+    MEMORY=$2
+    shift # past argument
+    shift # past value
+    ;;
     --offline)
     OFFLINE="--offline"
     shift # past value
@@ -44,9 +50,9 @@ do
 done
 
 # Build references for smallGRCh37
-if ! [[ ANNOTATESNPEFF,ANNOTATEVEP =~ $TEST ]]
+if ! [[ ANNOTATEBOTH,ANNOTATESNPEFF,ANNOTATEVEP,LINT =~ $TEST ]]
  then
   rm -rf references
-  nextflow run ${TRAVIS_BUILD_DIR}/build.nf -profile test,${PROFILE} --build --outdir references ${VERBOSE} ${OFFLINE}
+  nextflow run ${TRAVIS_BUILD_DIR}/build.nf -profile test,${PROFILE} --build --outdir references ${VERBOSE} ${OFFLINE} --max_memory ${MEMORY}
   rm -rf .nextflow* references/pipeline_info work
 fi

scripts/download_image.sh

@@ -74,7 +74,7 @@ then
   get_image sarekvep ${VERSION}.${SOURCEGENOME} ${VERSION}.${GENOME}
 fi
 
-if ! [[ ANNOTATEBOTH,ANNOTATESNPEFF,ANNOTATEVEP,SNPEFF,VEP =~ $TEST ]]
+if ! [[ ANNOTATEBOTH,ANNOTATESNPEFF,ANNOTATEVEP,LINT,SNPEFF,VEP =~ $TEST ]]
 then
   get_image sarek ${VERSION} ${VERSION}
 fi

scripts/run_tests.sh

@@ -4,14 +4,15 @@ set -xeuo pipefail
 # This script run sarek tests
 # https://github.com/nf-core/test-datasets/raw/sarek
 
-usage() { echo "Usage: $0 <-p profile> <-t test> <-c cpus> <-n> <-v>" 1>&2; exit 1; }
+usage() { echo "Usage: $0 <-p profile> <-t test> <-c cpus> <-n> <-v> <-m memory>" 1>&2; exit 1; }
 
 CPUS=2
 LOGS=''
-REPORTS=''
+MEMORY='7.GB'
 NXF_SINGULARITY_CACHEDIR=${NXF_SINGULARITY_CACHEDIR:-work/singularity/.}
 OFFLINE=false
 PROFILE=docker
+REPORTS=''
 TEST=MULTIPLE
 TRAVIS=${TRAVIS:-false}
 TRAVIS_BUILD_DIR=${TRAVIS_BUILD_DIR:-.}
@@ -25,6 +26,11 @@ do
     CPUS=$2
     shift # past value
     ;;
+    -m|--memory)
+    MEMORY=$2
+    shift # past argument
+    shift # past value
+    ;;
     -n|--no-logs)
     LOGS=true
     shift # past value
@@ -66,7 +72,7 @@ function manage_logs() {
 }
 
 function run_sarek() {
-  nextflow run ${TRAVIS_BUILD_DIR}/main.nf -profile test,${PROFILE} ${VERBOSE} --monochrome_logs ${REPORTS} $@
+  nextflow run ${TRAVIS_BUILD_DIR}/main.nf -profile test,${PROFILE} ${VERBOSE} --monochrome_logs ${REPORTS} --max_memory ${MEMORY} $@
 }
 
 if [[ $OFFLINE == false ]]