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Merge pull request #222 from MaxUlysse/2.6.1
2.6.1
2 parents 75fe254 + e6b97db commit bce378e

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‎.circleci/config.yml

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environment:
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GENOME: GRCh37
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SNPEFF_CACHE_VERSION: "75"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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steps:
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- checkout
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- setup_remote_docker
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environment:
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GENOME: GRCh38
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SNPEFF_CACHE_VERSION: "86"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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snpeffgrcm38:
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<< : *buildsnpeff
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environment:
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GENOME: GRCm38
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SNPEFF_CACHE_VERSION: "86"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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snpeffcanfam3_1:
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<< : *buildsnpeff
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environment:
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GENOME: CanFam3.1
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SNPEFF_CACHE_VERSION: "86"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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snpeffwbcel235:
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<< : *buildsnpeff
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environment:
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GENOME: WBcel235
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SNPEFF_CACHE_VERSION: "86"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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vepgrch37: &buildvep
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docker:
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GENOME: GRCh37
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SPECIES: homo_sapiens
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VEP_VERSION: "99"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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steps:
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- checkout
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- setup_remote_docker
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no_output_timeout: 3h
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- run:
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command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:${SAREK_TAG}.${GENOME}
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no_output_timeout: 30m
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vepgrch38:
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<< : *buildvep
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environment:
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GENOME: GRCh38
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SPECIES: homo_sapiens
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VEP_VERSION: "99"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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vepgrcm38:
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<< : *buildvep
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environment:
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GENOME: GRCm38
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SPECIES: mus_musculus
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VEP_VERSION: "99"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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vepcanfam3_1:
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<< : *buildvep
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environment:
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GENOME: CanFam3.1
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SPECIES: canis_familiaris
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VEP_VERSION: "99"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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vepwbcel235:
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<< : *buildvep
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environment:
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GENOME: WBcel235
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SPECIES: caenorhabditis_elegans
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VEP_VERSION: "99"
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SAREK_TAG: 2.6
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SAREK_TAG: "2.6.1"
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workflows:
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version: 2

‎.github/workflows/awsfulltest.yml

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name: nf-core AWS full test
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# This workflow is triggered on push to the master branch and on published releases.
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# It runs the -profile 'test_full' on AWS batch
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on:
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release:
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types: [published]
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jobs:
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run-awstest:
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if: github.repository == 'nf-core/sarek'
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name: Run AWS full tests
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runs-on: ubuntu-latest
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steps:
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- name: Setup Miniconda
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uses: goanpeca/setup-miniconda@v1.0.2
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with:
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auto-update-conda: true
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python-version: 3.7
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- name: Install awscli
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run: conda install -c conda-forge awscli
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- name: Start AWS batch job
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# TODO nf-core: You can customise AWS full pipeline tests as required
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# Add full size test data (but still relatively small datasets for few samples)
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# on the `test_full.config` test runs with only one set of parameters
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# Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
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env:
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AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
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AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
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TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
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AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
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AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
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AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
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run: |
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aws batch submit-job \
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--region eu-west-1 \
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--job-name nf-core-sarek \
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--job-queue $AWS_JOB_QUEUE \
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--job-definition $AWS_JOB_DEFINITION \
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--container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

‎.github/workflows/awstest.yml

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push:
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branches:
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- master
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release:
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types: [published]
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jobs:
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run-awstest:
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if: github.repository == 'nf-core/sarek'
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name: Run AWS test
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runs-on: ubuntu-latest
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steps:
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run: conda install -c conda-forge awscli
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- name: Start AWS batch job
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env:
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AWS_ACCESS_KEY_ID: ${{secrets.AWS_KEY_ID}}
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AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_KEY_SECRET}}
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TOWER_ACCESS_TOKEN: ${{secrets.TOWER_ACCESS_TOKEN}}
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AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
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AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
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TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
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AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
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AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
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AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
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run: |
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aws batch submit-job --region eu-west-1 --job-name nf-core-sarek --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' --job-definition nextflow --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://nf-core-awsmegatests/sarek/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
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aws batch submit-job \
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--region eu-west-1 \
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--job-name nf-core-sarek \
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--job-queue $AWS_JOB_QUEUE \
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--job-definition $AWS_JOB_DEFINITION \
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--container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

‎.github/workflows/ci.yml

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- name: Pull docker 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:2.6
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docker tag nfcore/sarek:dev nfcore/sarek:2.6.1
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- name: Run test
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run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker
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NXF_VER: '19.10.0'
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- name: Pull docker image
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run: |
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docker pull nfcore/sarek:2.6
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docker pull nfcore/sarek${{ matrix.tools }}:2.6.${{ matrix.species }}
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docker pull nfcore/sarek:2.6.1
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docker pull nfcore/sarek${{ matrix.tools }}:2.6.1.${{ matrix.species }}
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- name: Run annotation test
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run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}
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# Only check Nextflow pipeline minimum version
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NXF_VER: '19.10.0'
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- name: Pull docker image
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run: docker pull nfcore/sarek:2.6
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run: docker pull nfcore/sarek:2.6.1
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- name: Get test data
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run: 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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# Only check Nextflow pipeline minimum version
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NXF_VER: '19.10.0'
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- name: Pull docker image
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run: docker pull nfcore/sarek:2.6
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run: docker pull nfcore/sarek:2.6.1
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- name: Run test for minimal genomes
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run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
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# Only check Nextflow pipeline minimum version
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NXF_VER: '19.10.0'
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- name: Pull docker image
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run: docker pull nfcore/sarek:2.6
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run: docker pull nfcore/sarek:2.6.1
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- name: Run ${{ matrix.profile }} test
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run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
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# Only check Nextflow pipeline minimum version
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NXF_VER: '19.10.0'
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- name: Pull docker image
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run: docker pull nfcore/sarek:2.6
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run: docker pull nfcore/sarek:2.6.1
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- name: Run ${{ matrix.tool }} test
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run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}

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