.gitlab-ci.yml

image: continuumio/miniconda3:latest

variables:
  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"

cache:
  key: one-key-to-rule-them-all
  paths:
    - .conda/
    - .cache/pip/

stages:
  - test_infrastructure
  - test_code
  - for_production

before_script:
  - export PIP_CACHE_DIR="/opt/cache/pip"
  - conda install -c conda-forge mamba
  - mamba create -c conda-forge -c bioconda -n snakemake snakemake=5.30 git-annex  #conda env create -f workflow/envs/snakemake-base.yml
  - source activate snakemake

# Test if snakmake is installed
test_snakemake:
  stage: test_infrastructure
  tags:
    - test
  script:
    - echo $ftp_proxy
    - snakemake --version

# Start the snakemake pipeline as a dry-run (-n)
test_pipeline:
  stage: test_code
  tags:
    - test
  script:
    - snakemake --use-conda -n -p --configfile=config/config.json --config genome_config=resources/examples/saccharomyces_cerevisiae.json ensembl_release=98

# Run the snakemake pipeline on the "review" runner, which creates genome files at a temporary location but not in the final
# directory with version control
review_pipeline:
  stage: test_code
  tags:
    - review
  script:
    - snakemake --use-conda  -p $CI_SNAKEMAKE_ARGS --configfile=config/config.json --config genome_config=resources/current.json ensembl_release=98

# Run the snakemake pipeline on the "production" runner, which creates genome files at the final location and commit it
# to version control w/ git annex
run_pipeline:
  stage: for_production
  tags:
    - production
  script:
    - snakemake --use-conda  -p $CI_SNAKEMAKE_ARGS --configfile=config/config.json --config genome_config=resources/current.json ensembl_release=98
    - cd /data/reference-data/public-data/ && git annex add /data/reference-data/public-data/
    - cd /data/reference-data/public-data/ && git commit -a -m "add genome" && echo "commit successful" || echo "commit unsucessful"