.gitlab-ci.yml

variables:
  GIT_SUBMODULE_STRATEGY: recursive

.docker_before_script_anchor: &docker_before_script_anchor
  before_script:
    - pip3 install -r requirements.txt
    - pip3 install -r requirements-dev.txt

.singularity_before_script_anchor: &singularity_before_script_anchor
  before_script:
    - export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
    - source ${CONDA_SH}
    - conda activate hutspot-pipeline
    - export PATH=${PATH}:${SINGULARITY_PATH}
    - echo "#!/usr/bin/env bash" > snakemake
    - echo "$(which snakemake) --profile slurm-test \"\$@\"" >> snakemake
    - chmod +x snakemake
    - export PATH=$(pwd):${PATH}
    - hash -r


stages:
  - sanity
  - dry-run
  - integration

test_sanities:
  <<: *docker_before_script_anchor
  script:
    - pytest --tag sanity --workflow-threads 8
  image: lumc/singularity-snakemake:3.5.2-5.15.0
  tags:
    - docker
  stage: sanity

test_dry_run:
  <<: *docker_before_script_anchor
  script:
    - pytest --tag dry-run --workflow-threads 8
  image: lumc/singularity-snakemake:3.5.2-5.15.0
  tags:
    - docker
  stage: dry-run


test_integration:
  <<: *singularity_before_script_anchor
  script:
    - pytest --tag integration --basetemp ${BASETEMP} --keep-workflow-wd --workflow-threads 8
  tags:
    - slurm
  stage: integration