.gitlab-ci.yml 2.38 KB
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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==0.7.1 pytest-cov==2.5.1
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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
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  - astrocyte
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  - single
  - multiple
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  - skip
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  - cleanup
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user_configuration:
  stage: unit
  script:
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  - pytest -m unit --cov=./workflow/scripts
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astrocyte:
  stage: astrocyte
  script:
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  - module load astrocyte/0.2.0
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  - module unload nextflow
  - cd ..
  - astrocyte_cli validate chipseq_analysis
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  after_script:
    - rm -rf work/
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single_end_mouse:
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  stage: single
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  only:
    - master
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  script:
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  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true
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  - pytest -m singleend
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paired_end_human:
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  stage: single
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  only:
    - branches
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  except:
    - master
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  script:
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  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
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  - pytest -m pairedend
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single_end_single_control:
  stage: single
  only:
    - branches
  except:
    - master
  script:
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  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
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  - pytest -m singlecontrol
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single_end_diff:
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  stage: multiple
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  only:
    - branches
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  except:
    - master
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  script:
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  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
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  - pytest -m singleend
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  - pytest -m singlediff
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paired_end_diff:
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  only:
    - master
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  stage: multiple
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  script:
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  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
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  - pytest -m pairedend
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  - pytest -m paireddiff
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single_end_skip:
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  stage: skip
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  only:
    - master
  script:
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  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false
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  - pytest -m singleskip_true
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cleanup_job:
  stage: cleanup
  script:
    - cd $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME
    - rm -fr $CI_PIPELINE_ID/