forked from nf-core/sarek
-
Notifications
You must be signed in to change notification settings - Fork 0
/
test_mpileup.yml
74 lines (74 loc) · 3 KB
/
test_mpileup.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
- name: Run variant calling on tumor_only sample to test mpileup
command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mpileup --outdir results
tags:
- tumor_only
- mpileup
files:
- path: results/multiqc
- path: results/variant_calling/bcftools/sample2/sample2.bcftools.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/bcftools/sample2/sample2.bcftools.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz
should_exist: false
- path: results/mpileup
should_exist: false
- name: Run variant calling on tumor_only sample to test mpileup without intervals
command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mpileup --no_intervals --outdir results
tags:
- tumor_only
- mpileup
- no_intervals
files:
- path: results/multiqc
- path: results/no_intervals.bed
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz.tbi
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/variant_calling/bcftools/sample2/sample2.bcftools.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/bcftools/sample2/sample2.bcftools.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/mpileup/
should_exist: false
- path: results/mpileup
should_exist: false
- name: Run variant calling on germline sample to test mpileup
command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --outdir results
tags:
- germline
- mpileup
files:
- path: results/multiqc
- path: results/variant_calling/bcftools/sample1/sample1.bcftools.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/bcftools/sample1/sample1.bcftools.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/mpileup/
should_exist: false
- path: results/mpileup
should_exist: false
- name: Run variant calling on germline sample to test mpileup without intervals
command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --no_intervals --outdir results
tags:
- germline
- mpileup
- no_intervals
files:
- path: results/multiqc
- path: results/no_intervals.bed
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz.tbi
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/variant_calling/bcftools/sample1/sample1.bcftools.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/bcftools/sample1/sample1.bcftools.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/mpileup/
should_exist: false
- path: results/mpileup
should_exist: false