.gitlab-ci.yml

image: continuumio/miniconda3:latest

variables:
    GIT_SUBMODULE_STRATEGY: normal

before_script:
  - conda config --set always_yes yes --set changeps1 no
  - conda info -a
  - conda config --add channels defaults
  - conda config --add channels bioconda
  - conda config --add channels conda-forge
  - conda create -q -n snakemake snakemake pygments mamba python=${PYTHON_VERSION}
  - conda create -q -n prep bwa=0.7.17 gatk4=4.0.5.1 samtools=1.9
  - source activate prep
  - bwa index .test/data/ref/genome.chr21.fa
  - samtools faidx .test/data/ref/genome.chr21.fa
  - gatk CreateSequenceDictionary -R .test/data/ref/genome.chr21.fa

tests:
  stage: test
  script:
    - source activate snakemake
    # run the workflow
    # put a test case into the subfolder .test (e.g., use https://gitlab.com/bu_cnio/ngs-test-data as a submodule)
    - snakemake --cores 4 --use-conda --directory .test
    - snakemake --cores 1 --directory .test --report report.html