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Merge pull request #74 from MaxUlysse/CLEANUP
Remove unused scripts and improve CI
2 parents e2b3101 + 5355c1e commit 0612068

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‎.github/workflows/ci-extra.yml‎

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‎.github/workflows/ci.yml‎

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@@ -21,4 +21,110 @@ jobs:
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docker tag nfcore/sarek:dev nfcore/sarek:dev
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- name: Run test
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker
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annotation:
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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annotator: [snpeff]
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specie: [GRCh37]
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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env:
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NXF_VER: '19.10.0'
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- name: Download and tag images
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run: |
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docker pull nfcore/sarek:dev
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docker tag nfcore/sarek:dev nfcore/sarek:dev
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docker pull nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
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docker tag nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }} nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
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- name: Run annotation test
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run: |
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nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.annotator }}
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germline:
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runs-on: ubuntu-18.04
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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env:
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NXF_VER: '19.10.0'
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- name: Download and tag image
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run: |
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docker pull nfcore/sarek:dev
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docker tag nfcore/sarek:dev nfcore/sarek:dev
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- name: Get test data
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run: |
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git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
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- name: Run germline test
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run: |
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nextflow run . -profile test,docker --input data/testdata/tiny/normal
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nextflow run . -profile test,docker --input=false --step recalibrate -resume
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nextflow run . -profile test,docker --input=false --step variantCalling
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minimal:
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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genome: [smallerGRCh37, minimalGRCh37]
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intervals: [--no_intervals, '']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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env:
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NXF_VER: '19.10.0'
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- name: Download and tag image
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run: |
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docker pull nfcore/sarek:dev
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docker tag nfcore/sarek:dev nfcore/sarek:dev
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- name: Run test for minimal genomes
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run: |
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nextflow run . -profile test,docker --skipQC all --verbose --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka
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profile:
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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profile: [test_splitfastq, test_targeted]
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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env:
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NXF_VER: '19.10.0'
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- name: Download and tag image
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run: |
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docker pull nfcore/sarek:dev
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docker tag nfcore/sarek:dev nfcore/sarek:dev
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- name: Run targeted and splitfastq tests
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run: |
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nextflow run . -profile ${{ matrix.profile }},docker --verbose
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tools:
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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tool: [Haplotypecaller, Freebayes, Manta, mpileup, Mutect2, Strelka]
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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env:
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NXF_VER: '19.10.0'
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- name: Download and tag image
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run: |
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docker pull nfcore/sarek:dev
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docker tag nfcore/sarek:dev nfcore/sarek:dev
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- name: Run vriant calling test on specific tools
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run: |
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nextflow run . -profile test_tool,docker --verbose --tools ${{ matrix.tool }}

‎CHANGELOG.md‎

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@@ -35,10 +35,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
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- [#60](https://github.com/nf-core/sarek/pull/60) - Update documentation
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- [#71](https://github.com/nf-core/sarek/pull/71) - Update `README`
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- [#71](https://github.com/nf-core/sarek/pull/71) - Update `CHANGELOG`
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- [#74](https://github.com/nf-core/sarek/pull/74) - Update docs
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- [#74](https://github.com/nf-core/sarek/pull/74) - Improve CI tests (both Jenkins and GitHub actions tests)
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- [#74](https://github.com/nf-core/sarek/pull/74) - Move all ci from `ci-extra.yml` to `ci.yml`
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### `Removed`
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- [#46](https://github.com/nf-core/sarek/pull/46) - Remove mention of old `build.nf` script which was included in `main.nf`
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- [#74](https://github.com/nf-core/sarek/pull/74) - Remove `download_image.sh` and `run_tests.sh` scripts
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### `Fixed`
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‎Jenkinsfile‎

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stages {
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stage('Docker setup') {
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steps {
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sh "./scripts/download_image.sh -n docker -t ALL --source-version dev --target-version dev -g smallGRCh37"
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sh "docker pull nfcore/sarek:dev"
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sh "docker tag nfcore/sarek:dev nfcore/sarek:dev"
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sh "docker pull nfcore/sareksnpeff:dev.GRCh37"
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sh "docker tag nfcore/sareksnpeff:dev.GRCh37 nfcore/sareksnpeff:dev.GRCh37"
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sh "docker pull nfcore/sarekvep:dev.GRCh37"
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sh "docker tag nfcore/sarekvep:dev.GRCh37 nfcore/sarekvep:dev.GRCh37"
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}
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}
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stage('Annotation') {
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steps {
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sh "nextflow run . -profile test_annotation,kraken --verbose --tools snpeff,vep,merge"
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}
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}
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stage('Germline') {
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steps {
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sh "rm -rf data/"
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sh "git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data"
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sh "./scripts/run_tests.sh --profile kraken --test GERMLINE --no-reports"
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sh "nextflow run . -profile test,kraken --input data/testdata/tiny/normal"
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sh "nextflow run . -profile test,kraken --input=false --step recalibrate -resume"
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sh "nextflow run . -profile test,kraken --input=false --step variantCalling"
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sh "rm -rf data/"
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}
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}
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stage('Somatic') {
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stage('Minimal') {
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steps {
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sh "./scripts/run_tests.sh --profile kraken --test SOMATIC --no-reports"
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sh "nextflow run . -profile test,kraken --skipQC all --verbose --genome smallerGRCh37 --no_intervals --tools Manta,mpileup,Strelka"
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sh "nextflow run . -profile test,kraken --skipQC all --verbose --genome smallerGRCh37 --tools Manta,mpileup,Strelka"
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sh "nextflow run . -profile test,kraken --skipQC all --verbose --genome minimalGRCh37 --no_intervals --tools Manta,mpileup,Strelka"
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sh "nextflow run . -profile test,kraken --skipQC all --verbose --genome minimalGRCh37 --tools Manta,mpileup,Strelka"
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}
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}
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stage('Targeted') {
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steps {
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sh "./scripts/run_tests.sh --profile kraken --test TARGETED --no-reports"
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}
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}
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stage('Annotation') {
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stage('Profile') {
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steps {
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sh "./scripts/run_tests.sh --profile kraken --test ANNOTATEBOTH --no-reports"
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sh "nextflow run . -profile test_splitfastq,kraken --verbose"
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sh "nextflow run . -profile test_targeted,kraken --verbose"
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}
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}
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stage('Multiple') {
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stage('Tools') {
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steps {
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sh "./scripts/run_tests.sh --profile kraken --test MULTIPLE"
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sh "nextflow run . -profile test_tool,kraken --verbose --tools Haplotypecaller,Freebayes,Manta,mpileup,Mutect2,Strelka"
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}
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}
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}

‎README.md‎

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[![DOI](https://zenodo.org/badge/184289291.svg)](https://zenodo.org/badge/latestdoi/184289291)
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[![GitHub Actions CI status](https://github.com/nf-core/sarek/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22sarek+CI%22)
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[![GitHub Actions extra-CI status](https://github.com/nf-core/sarek/workflows/nf-core%20extra%20CI/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22sarek+extra+CI%22)
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[![GitHub Actions Linting status](https://github.com/nf-core/sarek/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22sarek+linting%22)
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[![CircleCi build status](https://img.shields.io/circleci/project/github/nf-core/sarek?logo=circleci)](https://circleci.com/gh/nf-core/sarek/)
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‎docs/annotation.md‎

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Example:
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```bash
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nextflow run nf-core/sarek/main.nf --tools snpEff --step annotate --sample file.vcf.gz --snpEff_cache /Path/To/snpEffCache --annotation_cache
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nextflow run nf-core/sarek/main.nf --tools VEP --step annotate --sample file.vcf.gz --vep_cache /Path/To/vepCache --annotation_cache
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nextflow run nf-core/sarek --tools snpEff --step annotate --sample file.vcf.gz --snpEff_cache /Path/To/snpEffCache --annotation_cache
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nextflow run nf-core/sarek --tools VEP --step annotate --sample file.vcf.gz --vep_cache /Path/To/vepCache --annotation_cache
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```
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## Using VEP CADD plugin
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Example:
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```bash
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nextflow run nf-core/sarek/main.nf --step annotate --tools VEP --sample file.vcf.gz --cadd_cache \
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nextflow run nf-core/sarek --step annotate --tools VEP --sample file.vcf.gz --cadd_cache \
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--cadd_InDels /PathToCADD/InDels.tsv.gz \
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--cadd_InDels_tbi /PathToCADD/InDels.tsv.gz.tbi \
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--cadd_WG_SNVs /PathToCADD/whole_genome_SNVs.tsv.gz \
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Example:
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```bash
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nextflow run nf-core/sarek/main.nf --step annotate --tools VEP --sample file.vcf.gz --genesplicer
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nextflow run nf-core/sarek --step annotate --tools VEP --sample file.vcf.gz --genesplicer
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```

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