config.yml

version: 2.0
jobs:
  snpeffgrch37: &buildsnpeff
    docker:
      - image: circleci/buildpack-deps:stretch
    environment:
      GENOME: GRCh37
      SNPEFF_CACHE_VERSION: "75"
      SAREK_TAG: 2.7.1
    steps:
      - checkout
      - setup_remote_docker
      - run:
          command: docker build -t nfcore/sareksnpeff:${SAREK_TAG}.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
      - run:
          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sareksnpeff:${SAREK_TAG}.${GENOME}

  snpeffgrch38:
    << : *buildsnpeff
    environment:
      GENOME: GRCh38
      SNPEFF_CACHE_VERSION: "86"
      SAREK_TAG: 2.7.1

  snpeffgrcm38:
    << : *buildsnpeff
    environment:
      GENOME: GRCm38
      SNPEFF_CACHE_VERSION: "86"
      SAREK_TAG: 2.7.1

  snpeffcanfam3_1:
    << : *buildsnpeff
    environment:
      GENOME: CanFam3.1
      SNPEFF_CACHE_VERSION: "86"
      SAREK_TAG: 2.7.1

  snpeffwbcel235:
    << : *buildsnpeff
    environment:
      GENOME: WBcel235
      SNPEFF_CACHE_VERSION: "86"
      SAREK_TAG: 2.7.1

  vepgrch37: &buildvep
    docker:
      - image: circleci/buildpack-deps:stretch
    environment:
      GENOME: GRCh37
      SPECIES: homo_sapiens
      VEP_VERSION: "99"
      SAREK_TAG: 2.7.1
    steps:
      - checkout
      - setup_remote_docker
      - run:
          command: docker build -t nfcore/sarekvep:${SAREK_TAG}.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
          no_output_timeout: 3h
      - run:
          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:${SAREK_TAG}.${GENOME}
          no_output_timeout: 30m

  vepgrch38:
    << : *buildvep
    environment:
      GENOME: GRCh38
      SPECIES: homo_sapiens
      VEP_VERSION: "99"
      SAREK_TAG: 2.7.1

  vepgrcm38:
    << : *buildvep
    environment:
      GENOME: GRCm38
      SPECIES: mus_musculus
      VEP_VERSION: "99"
      SAREK_TAG: 2.7.1

  vepcanfam3_1:
    << : *buildvep
    environment:
      GENOME: CanFam3.1
      SPECIES: canis_familiaris
      VEP_VERSION: "99"
      SAREK_TAG: 2.7.1

  vepwbcel235:
    << : *buildvep
    environment:
      GENOME: WBcel235
      SPECIES: caenorhabditis_elegans
      VEP_VERSION: "99"
      SAREK_TAG: 2.7.1

workflows:
  version: 2
  build:
    jobs:
      - snpeffcanfam3_1
      - snpeffgrch37
      - snpeffgrch38
      - snpeffgrcm38
      - snpeffwbcel235
      - vepcanfam3_1
      - vepgrch37
      - vepgrch38
      - vepgrcm38
      - vepwbcel235