.gitlab-ci.yml 589 Bytes
Newer Older
Venkat Malladi's avatar
Venkat Malladi committed
1
before_script:
Venkat Malladi's avatar
Venkat Malladi committed
2
  - module add  python/3.6.1-2-anaconda
3
  - pip install --user pytest-pythonpath
Venkat Malladi's avatar
Venkat Malladi committed
4
5
  - module load nextflow/0.24.1-SNAPSHOT
  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
Venkat Malladi's avatar
Venkat Malladi committed
6

Venkat Malladi's avatar
Venkat Malladi committed
7
8
9
10
11
12
13
14
15
16
17
18
19
stages:
  - unit
  - integration

user_configuration:
  stage: unit
  script:
  - pytest -m unit

single_end_mouse:
  stage: integration
  script:
  - nextflow run workflow/main.nf
20
  - pytest -m integration
Venkat Malladi's avatar
Venkat Malladi committed
21
22
23
24
25

paired_end_human:
  stage: integration
  script:
  - nextflow run workflow/main.nf --designFile "test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'