.gitlab-ci.yml 768 Bytes
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# Gitlab CI Script for astrocyte/rnaseq
# Brandi L. Cantarel - 2017

variables:
  TEST_BRANCH: "master"
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  GIT_SUBMODULE_STATEGY: recursive
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before_script:
  - module load nextflow/0.27.6
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  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq test_data
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stages:
  - integration

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test_human:
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  stage: integration
  script:
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    - nextflow run workflow/main.nf --design test_data/design.rnaseq.txt --input test_data --output human_output
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  artifacts:
    expire_in: 2 days

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test_mouse:
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  stage: integration
  script:
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    - nextflow run workflow/main.nf --input test_data --design test_data/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output mouse_output
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  artifacts:
    expire_in: 2 days