Nf core vc

.circleci/config.yml

@@ -0,0 +1,111 @@
+version: 2.0
+jobs:
+  snpeffgrch37:
+    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:dev.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+      - run:
+          command: |
+            echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+            docker push nfcore/sareksnpeff:dev.${GENOME}
+
+  snpeffgrch38:
+    docker:
+      - image: circleci/buildpack-deps:stretch
+    environment:
+      GENOME: GRCh38
+      SNPEFF_CACHE_VERSION: 86
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          command: docker build -t nfcore/sareksnpeff:dev.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+      - run:
+          command: |
+            echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+            docker push nfcore/sareksnpeff:dev.${GENOME}
+
+  snpeffgrcm38:
+    docker:
+      - image: circleci/buildpack-deps:stretch
+    environment:
+      GENOME: GRCm38
+      SNPEFF_CACHE_VERSION: 86
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          command: docker build -t nfcore/sareksnpeff:dev.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+      - run:
+          command: |
+            echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+            docker push nfcore/sareksnpeff:dev.${GENOME}
+
+  vepgrch37:
+    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:dev.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          no_output_timeout: 45m
+      - run:
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:dev.${GENOME}
+          no_output_timeout: 45m
+
+  vepgrch38:
+    docker:
+      - image: circleci/buildpack-deps:stretch
+    environment:
+      GENOME: GRCh38
+      SPECIES: homo_sapiens
+      VEP_VERSION: 95
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          command: docker build -t nfcore/sarekvep:dev.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          no_output_timeout: 45m
+      - run:
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:dev.${GENOME}
+          no_output_timeout: 45m
+
+  vepgrcm38:
+    docker:
+      - image: circleci/buildpack-deps:stretch
+    environment:
+      GENOME: GRCm38
+      SPECIES: mus_musculus
+      VEP_VERSION: 95
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          command: docker build -t nfcore/sarekvep:dev.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          no_output_timeout: 45m
+      - run:
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:dev.${GENOME}
+          no_output_timeout: 45m
+
+workflows:
+  version: 2
+  build:
+    jobs:
+      - snpeffgrch37
+      - snpeffgrch38
+      - snpeffgrcm38
+      - vepgrch37
+      - vepgrch38
+      - vepgrcm38

.travis.yml

@@ -14,15 +14,20 @@ matrix:
   fast_finish: true
 
 env:
-  - NXF_VER=19.04.0
+  global:
+    - NXF_VER=19.04.0
+  matrix:
+    - TEST=SOMATIC
+    - TEST=GERMLINE
+    - TEST=TARGETED
+    - TEST=ANNOTATEVEP
+    - TEST=ANNOTATESNPEFF
 
 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
-  - docker pull nfcore/sarek:dev
-  # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/sarek:dev nfcore/sarek:dev
+  - "travis_retry ./bin/download_docker.sh --test $TEST"
 
 install:
   # Install Nextflow
@@ -32,7 +37,10 @@ install:
   # Reset
   - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
 
+# Build references if needed
+before_script:
+  - "${TRAVIS_BUILD_DIR}/bin/build_reference.sh --test $TEST --build"
+
+# Actual tests
 script:
-  - git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
-  - nextflow run ${TRAVIS_BUILD_DIR}/build.nf -profile docker --genome smallGRCh37 --refdir data/reference --outdir references --publishDirMode link --max_memory 7.GB --max_cpus 2 -ansi-log false
-  - nextflow run ${TRAVIS_BUILD_DIR}/main.nf -profile docker --genome smallGRCh37 --sample data/testdata/tsv/tiny-manta.tsv --tools HaploTypeCaller,Manta,Strelka,MuTecT2,FreeBayes --igenomes_base references --publishDirMode link --max_memory 7.GB --max_cpus 2 -ansi-log false
+  - "${TRAVIS_BUILD_DIR}/bin/run_tests.sh --test $TEST"

Jenkinsfile

@@ -8,26 +8,43 @@ pipeline {
     stages {
         stage('Setup environment') {
             steps {
-                sh "docker pull nfcore/sarek:dev"
+                sh "./bin/download_docker.sh -t ALL"
             }
         }
         stage('Build') {
             steps {
                 sh "rm -rf data"
-                sh "git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data"
-                sh "nextflow run build.nf -profile docker --genome smallGRCh37 --refdir data/reference --outdir references --publishDirMode link -ansi-log false"
+                sh "./bin/build_reference.sh --test ALL --build"
                 sh "rm -rf work/ references/pipeline_info .nextflow*"
             }
         }
-        stage('SampleDir') {
+        stage('Somatic') {
             steps {
-                sh "nextflow run main.nf -profile docker --sampleDir data/testdata/tiny/normal --tools HaplotypeCaller,Manta,Strelka --genome smallGRCh37 --igenomes_base references --publishDirMode link -ansi-log false"
+                sh "./bin/run_tests.sh --test SOMATIC"
+                sh "rm -rf work/ .nextflow* results/"
+            }
+        }
+        stage('Germline') {
+            steps {
+                sh "./bin/run_tests.sh --test GERMLINE"
+                sh "rm -rf work/ .nextflow* results/"
+            }
+        }
+        stage('targeted') {
+            steps {
+                sh "./bin/run_tests.sh --test TARGETED"
+                sh "rm -rf work/ .nextflow* results/"
+            }
+        }
+        stage('Annotation') {
+            steps {
+                sh "./bin/run_tests.sh --test ANNOTATEALL"
                 sh "rm -rf work/ .nextflow* results/"
             }
         }
         stage('Multiple') {
             steps {
-                sh "nextflow run main.nf -profile docker --sample data/testdata/tsv/tiny-multiple.tsv --tools HaploTypeCaller,Manta,Strelka,MuTecT2,FreeBayes --genome smallGRCh37 --igenomes_base references --publishDirMode link -ansi-log false"
+                sh "./bin/run_tests.sh --test MULTIPLE"
                 sh "rm -rf work/ .nextflow* results/"
             }
         }

README.md

@@ -7,9 +7,11 @@
 
 [![Nextflow version][nextflow-badge]](https://www.nextflow.io)
 [![Travis build status][travis-badge]](https://travis-ci.org/nf-core/sarek)
+[![CircleCi build status][circleci-badge]](https://circleci.com/gh/nf-core/workflows/sarek)
 
 [![Install with bioconda][bioconda-badge]](http://bioconda.github.io/)
-[![Docker Container available][docker-badge]](https://hub.docker.com/r/nfcore/sarek)
+[![Docker Container available][docker-sarek-badge]](https://hub.docker.com/r/nfcore/sarek)
+[![Install with Singularity][singularity-badge]](https://www.sylabs.io/docs/)
 
 [![Join us on Slack][slack-badge]](https://nfcore.slack.com/messages/CGFUX04HZ/)
 
@@ -77,7 +79,7 @@ The worflow steps and tools used are as follows:
         * [GATK ApplyBQSR](https://github.com/broadinstitute/gatk)
 2. **Germline variant calling** - `germlineVC.nf`
     * SNVs and small indels
-        * [GATK HaplotyeCaller](https://github.com/broadinstitute/gatk)
+        * [GATK HaplotypeCaller](https://github.com/broadinstitute/gatk)
         * [Strelka2](https://github.com/Illumina/strelka)
     * Structural variants
         * [Manta](https://github.com/Illumina/manta)
@@ -139,10 +141,14 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 
 [bioconda-badge]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?logo=data:image/png;base64,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
 [btb-link]: https://ki.se/forskning/barntumorbanken-0
-[docker-badge]: https://img.shields.io/docker/automated/nfcore/sarek.svg?logo=docker
+[circleci-badge]: https://img.shields.io/circleci/project/github/nf-core/sarek.svg?logo=circleci
+[docker-sarek-badge]: https://img.shields.io/docker/automated/nfcore/sarek.svg?logo=docker
+[docker-snpeff-badge]: https://img.shields.io/docker/automated/nfcore/sareksnpeff.svg?logo=docker
+[docker-vep-badge]: https://img.shields.io/docker/automated/nfcore/sarekvep.svg?logo=docker
 [nbis-link]: https://nbis.se
 [nextflow-badge]: https://img.shields.io/badge/nextflow-%E2%89%A519.04.0-brightgreen.svg?logo=data:image/svg+xml;base64,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
 [ngi-link]: https://ngisweden.scilifelab.se/
 [scilifelab-link]: https://scilifelab.se
+[singularity-badge]: https://img.shields.io/badge/use%20with-singularity-purple.svg
 [slack-badge]: https://img.shields.io/badge/slack-nfcore/sarek-blue.svg?logo=slack
 [travis-badge]: https://img.shields.io/travis/nf-core/sarek.svg?logo=travis

bin/build_reference.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+set -xeuo pipefail
+
+BUILD=false
+TEST=ALL
+TRAVIS_BUILD_DIR=${TRAVIS_BUILD_DIR:-.}
+TRAVIS=${TRAVIS:-false}
+
+while [[ $# -gt 0 ]]
+do
+  key=$1
+  case $key in
+    -t|--test)
+    TEST=$2
+    shift # past argument
+    shift # past value
+    ;;
+    -b|--build)
+    BUILD=true
+    shift # past value
+    ;;
+    *) # unknown option
+    shift # past argument
+    ;;
+  esac
+done
+
+# Always download test data
+rm -rf data
+git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
+
+# Build references for smallGRCh37
+if [[ BUILD ]] && [[ $TEST != ANNOTATESNPEFF ]] && [[ $TEST != ANNOTATEVEP ]]
+then
+  rm -rf references
+  nextflow run ${TRAVIS_BUILD_DIR}/build.nf -profile docker -ansi-log false --publishDirMode link --max_memory 7.GB --max_cpus 2 -dump-channels --genome smallGRCh37 --refdir data/reference --outdir references
+  rm -rf .nextflow* references/pipeline_info work
+fi

bin/download_docker.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+set -xeuo pipefail
+
+TEST=ALL
+
+while [[ $# -gt 0 ]]
+do
+  key=$1
+  case $key in
+    -t|--test)
+    TEST=$2
+    shift # past argument
+    shift # past value
+    ;;
+    *) # unknown option
+    shift # past argument
+    ;;
+  esac
+done
+
+if [[ ALL,ANNOTATEALL,ANNOTATEVEP =~ $TEST ]]
+then
+  docker pull nfcore/sarekvep:dev.GRCh37
+  docker tag nfcore/sarekvep:dev.GRCh37 nfcore/sarekvep:dev.smallGRCh37
+elif [[ ALL,ANNOTATEALL,ANNOTATESNPEFF =~ $TEST ]]
+then
+  docker pull nfcore/sareksnpeff:dev.GRCh37
+  docker tag nfcore/sareksnpeff:dev.GRCh37 nfcore/sareksnpeff:dev.smallGRCh37
+else
+  docker pull nfcore/sarek:dev
+  docker tag nfcore/sarek:dev nfcore/sarek:dev
+fi

bin/run_tests.sh

@@ -0,0 +1,66 @@
+#!/bin/bash
+set -xeuo pipefail
+
+CPUS=2
+TEST=ALL
+TRAVIS_BUILD_DIR=${TRAVIS_BUILD_DIR:-.}
+TRAVIS=${TRAVIS:-false}
+
+while [[ $# -gt 0 ]]
+do
+  key=$1
+  case $key in
+    -t|--test)
+    TEST=$2
+    shift # past argument
+    shift # past value
+    ;;
+    -c|--cpus)
+    CPUS=$2
+    shift # past value
+    ;;
+    *) # unknown option
+    shift # past argument
+    ;;
+  esac
+done
+
+function run_sarek() {
+  nextflow run ${TRAVIS_BUILD_DIR}/main.nf -profile docker -ansi-log false --publishDirMode link --max_memory 7.GB --max_cpus 2 -dump-channels --genome smallGRCh37 --igenomes_base references $@
+}
+
+if [[ ALL,GERMLINE =~ $TEST ]]
+then
+  run_sarek --sample data/testdata/tiny/normal --tools HaplotypeCaller,Strelka --noReports
+  run_sarek --step recalibrate --noReports
+fi
+
+if [[ ALL,SOMATIC =~ $TEST ]]
+then
+	run_sarek --sample data/testdata/tsv/tiny-manta.tsv --tools FreeBayes,HaplotypeCaller,Manta,Strelka,Mutect2 --noReports
+fi
+
+if [[ ALL,TARGETED =~ $TEST ]]
+then
+	run_sarek --sample data/testdata/tsv/tiny-manta.tsv --tools FreeBayes,HaplotypeCaller,Manta,Strelka,Mutect2 --noReports --targetBED data/testdata/target.bed
+fi
+
+if [[ ALL,ANNOTATEALL,ANNOTATESNPEFF,ANNOTATEVEP =~ $TEST ]]
+then
+  if [[ $TEST = ANNOTATESNPEFF ]]
+  then
+    ANNOTATOR=snpEFF
+  elif [[ $TEST = ANNOTATEVEP ]]
+  then
+    ANNOTATOR=VEP
+  elif [[ ALL,ANNOTATEALL =~ $TEST ]]
+  then
+    ANNOTATOR=merge,snpEFF,VEP
+  fi
+  run_sarek --step annotate --tools ${ANNOTATOR} --annotateVCF data/testdata/vcf/Strelka_1234N_variants.vcf.gz --noReports
+fi
+
+if [[ MULTIPLE =~ $TEST ]]
+then
+  run_sarek --sample data/testdata/tsv/tiny-multiple.tsv --tools FreeBayes,HaplotypeCaller,Manta,Strelka,Mutect2 --noReports
+fi