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* Add Annotation * Annotation containers are tagged version.genomeversion * Better indentation * Replace `--sampleDir` by `--sample` * add MultiQC * update Tests * Add parallelized testing on Travis * Add parallelized building of Docker Images for annotation on CircleCI * Update docs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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.${GENOME} | ||
| no_output_timeout: 45m | ||
|
|
||
| workflows: | ||
| version: 2 | ||
| build: | ||
| jobs: | ||
| - snpeffgrch37 | ||
| - snpeffgrch38 | ||
| - snpeffgrcm38 | ||
| - vepgrch37 | ||
| - vepgrch38 | ||
| - vepgrcm38 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| #!/bin/bash | ||
| set -xeuo pipefail | ||
|
|
||
| BUILD=false | ||
| TEST=ALL | ||
| TRAVIS_BUILD_DIR=${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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 =~ $TEST ]] | ||
| then | ||
| docker pull nfcore/sareksnpeff:dev.GRCh37 | ||
| docker tag nfcore/sareksnpeff:dev.GRCh37 nfcore/sareksnpeff:dev.smallGRCh37 | ||
| else | ||
| docker pull nfcore/sarek:dev | ||
| docker tag nfcore/sarek:dev nfcore/sarek:dev | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| #!/bin/bash | ||
| set -xeuo pipefail | ||
|
|
||
| CPUS=2 | ||
| TEST=ALL | ||
| TRAVIS_BUILD_DIR=${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 |
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