-
Notifications
You must be signed in to change notification settings - Fork 4
/
.gitlab-ci.yml
94 lines (84 loc) · 2.61 KB
/
.gitlab-ci.yml
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
86
87
88
89
90
91
92
93
94
variables:
GIT_SUBMODULE_STRATEGY: recursive
.slurm_before_script_anchor: &slurm_before_script_anchor
before_script:
- export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
- source ${CONDA_SH}
- conda activate HAMLET
- export PATH=${PATH}:${SINGULARITY_PATH}
- echo "#!/usr/bin/env bash" > snakemake
- echo "$(which snakemake) --profile slurm-test \"\$@\"" >> snakemake
- chmod +x snakemake
- export PATH=$(pwd):${PATH}
- echo $PATH
- echo $BASETEMP
- hash -r
stages:
- sanity
- dry-run
- integration
- report
test_sanity:
<<: *slurm_before_script_anchor
script:
- pytest --tag sanity --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: sanity
test_dry_run:
<<: *slurm_before_script_anchor
script:
- pytest --tag dry-run --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: dry-run
qc_seq:
<<: *slurm_before_script_anchor
script:
- pytest --tag integration --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail test/test_qc_seq.yml
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: integration
snv_indels:
<<: *slurm_before_script_anchor
script:
- pytest --tag integration --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail test/test_snv_indels.yml
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: integration
expression:
<<: *slurm_before_script_anchor
script:
- pytest --tag integration --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail test/test_expression.yml
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: integration
fusion:
<<: *slurm_before_script_anchor
script:
- pytest --tag integration --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail test/test_fusion.yml
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: integration
itd:
<<: *slurm_before_script_anchor
script:
- pytest --tag integration --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail test/test_itd.yml
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: integration
hamlet_report:
<<: *slurm_before_script_anchor
script:
- pytest --tag integration --basetemp ${BASETEMP} --workflow-threads 12 --keep-workflow-wd-on-fail test/test_hamlet.yml
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
stage: report