.gitlab-ci.yml

# CI pipeline to check astrocyte validity and pipeline status against
# human and barnyard data.

stages:
  - astrocyte
  - test

workflow:
  rules: 
    - if: $CI_COMMIT_TAG  # Only run on tagged commits

variables:
  GIT_STRATEGY: clone     # Set to avoid expected shallow list error
  GIT_DEPTH: 10           # Set to avoid expected shallow list error

astrocyte_check:    # Check for astrocyte validity
  stage: astrocyte
  tags: 
    - astrocyte
  script: 
    - module load astrocyte/2.0.1
    - astrocyte_cli check .

test-count-multisample:   # Run cellranger count on both human and mouse data
  stage: test
  needs: []
  tags:
    - vm
  before_script:
     - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
  script:
    - >
      nextflow run workflow/main.nf
      --sample_sheet=/data/test_data/sample_sheet.csv
      --fastq=/data/test_data/Brain_Tumor_3p_LT_fastqs
      --noBam=true
    - nextflow clean -f -keep-logs