.gitlab-ci.yml 2.01 KB
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==0.7.1 pytest-cov==2.5.1
4
  - module load nextflow/0.31.0
5
  - 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
stages:
  - unit
9
  - astrocyte
10
11
  - single
  - multiple
Venkat Malladi's avatar
Venkat Malladi committed
12
  - skip
Venkat Malladi's avatar
Venkat Malladi committed
13
14
15
16

user_configuration:
  stage: unit
  script:
Venkat Malladi's avatar
Venkat Malladi committed
17
  - pytest -m unit --cov=./workflow/scripts
Venkat Malladi's avatar
Venkat Malladi committed
18

19
20
21
22
23
24
25
26
astrocyte:
  stage: astrocyte
  script:
  - module load astrocyte/0.1.0
  - module unload nextflow
  - cd ..
  - astrocyte_cli validate chipseq_analysis

Venkat Malladi's avatar
Venkat Malladi committed
27
single_end_mouse:
28
  stage: single
29
30
  only:
    - master
Venkat Malladi's avatar
Venkat Malladi committed
31
  script:
Venkat Malladi's avatar
Venkat Malladi committed
32
  - nextflow run workflow/main.nf --astrocyte true
33
  - pytest -m singleend
Venkat Malladi's avatar
Venkat Malladi committed
34
35

paired_end_human:
36
  stage: single
37
38
  only:
    - branches
Venkat Malladi's avatar
Venkat Malladi committed
39
40
  except:
    - master
Venkat Malladi's avatar
Venkat Malladi committed
41
  script:
Venkat Malladi's avatar
Venkat Malladi committed
42
  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
43
  - pytest -m pairedend
44

45
46
47
48
49
50
51
single_end_single_control:
  stage: single
  only:
    - branches
  except:
    - master
  script:
Venkat Malladi's avatar
Venkat Malladi committed
52
  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
53
54
  - pytest -m singlecontrol
  
55
single_end_diff:
56
  stage: multiple
57
58
  only:
    - branches
Venkat Malladi's avatar
Venkat Malladi committed
59
60
  except:
    - master
61
  script:
Venkat Malladi's avatar
Venkat Malladi committed
62
  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
63
  - pytest -m singleend
Venkat Malladi's avatar
Venkat Malladi committed
64
  - pytest -m singlediff
65
66

paired_end_diff:
67
68
  only:
    - master
69
  stage: multiple
70
  script:
Venkat Malladi's avatar
Venkat Malladi committed
71
  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
72
  - pytest -m pairedend
Venkat Malladi's avatar
Venkat Malladi committed
73
  - pytest -m paireddiff
74
75

single_end_skip:
Venkat Malladi's avatar
Venkat Malladi committed
76
  stage: skip
77
78
79
  only:
    - master
  script:
Venkat Malladi's avatar
Venkat Malladi committed
80
  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false
Venkat Malladi's avatar
Venkat Malladi committed
81
  - pytest -m singleskip_true