.gitlab-ci.yml 800 Bytes
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before_script:
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  - module add  python/3.6.1-2-anaconda
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  - pip install --user pytest-pythonpath pytest-cov
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  - module load  nextflow/0.31.0
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  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
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stages:
  - unit
  - integration

user_configuration:
  stage: unit
  script:
  - pytest -m unit

single_end_mouse:
  stage: integration
  script:
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  - nextflow run workflow/main.nf -resume
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  - pytest -m integration
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  - pytest --cov=./workflow/scripts
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  artifacts:
    expire_in: 2 days
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paired_end_human:
  stage: integration
  script:
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  - nextflow run workflow/main.nf --designFile "/work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
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  artifacts:
    expire_in: 2 days