# Gitlab CI Script for astrocyte/rnaseq
# Brandi L. Cantarel - 2017

variables:
  CLEAN_REPO_PATH: "/project/BICF/BICF_Core/s166458/astrocyte_test/${CI_RUNNER_ID}"
  TEST_BRANCH: "master"

before_script:
  - module load nextflow/0.27.6
  - mkdir -p "${CLEAN_REPO_PATH}"
  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq ${CLEAN_REPO_PATH}/test_data

stages:
  - integration

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

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