sarek/.circleci/config.yml at 5c30fd821ab7cdf27fd4105464a1fba5eabdfcd5 · nf-core/sarek · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
version: 2.0
jobs:
  snpeffgrch37: &buildsnpeff
    docker:
      - image: circleci/buildpack-deps:stretch
    environment:
      GENOME: GRCh37
      SNPEFF_CACHE_VERSION: "75"
    steps:
      - checkout
      - setup_remote_docker
      - run:
          command: docker build -t nfcore/sareksnpeff:2.5.2.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
      - run:
          command: |
            echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
            docker push nfcore/sareksnpeff:2.5.2.${GENOME}

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

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

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

  vepgrch37: &buildvep
    docker:
      - image: circleci/buildpack-deps:stretch
    environment:
      GENOME: GRCh37
      SPECIES: homo_sapiens
      VEP_VERSION: "95"
    steps:
      - checkout
      - setup_remote_docker
      - run:
          command: docker build -t nfcore/sarekvep:2.5.2.${GENOME} containers/vep/. --build-arg GENOME=${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:2.5.2.${GENOME}

  vepgrch38:
    << : *buildvep
    environment:
      GENOME: GRCh38
      SPECIES: homo_sapiens
      VEP_VERSION: "95"

  vepgrcm38:
    << : *buildvep
    environment:
      GENOME: GRCm38
      SPECIES: mus_musculus
      VEP_VERSION: "95"

  vepcanfam3_1:
    << : *buildvep
    environment:
      GENOME: CanFam3.1
      SPECIES: canis_familiaris
      VEP_VERSION: "95"

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