forked from nf-core/sarek
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathtest_recalibrate_from_cram.yml
86 lines (86 loc) · 4.21 KB
/
test_recalibrate_from_cram.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
- name: Run Recalibration starting from cram
command: nextflow run main.nf -profile test,recalibrate_cram
tags:
- input_cram
- recalibrate
- preprocessing
files:
- path: results/csv/recalibrated.csv
md5sum: 1888a924bc70bd80165a96ad641e22d6
- path: results/multiqc
- path: results/preprocessing/recalibrated/test/test.recal.cram
# binary changes md5sums on reruns.
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns.
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test.
- path: results/preprocessing/mapped/
should_exist: false
- path: results/preprocessing/markduplicates/
should_exist: false
- name: Run Recalibration starting from cram and skip baserecalibration
command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr --tools strelka
tags:
- input_cram
- recalibrate
- preprocessing
- variant_calling
files:
- path: results/csv/variantcalled.csv
md5sum: 4d0effd3d8dc2b814230a189e7ca9dba
- path: results/multiqc
- path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
# conda changes md5sums for test.
- path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
md5sum: 39ff2cc8eb7495a14a6b76e0ab627027
- path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
md5sum: ee7dafc8d941b8502a04a63dc3126fff
- path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
# The text-based file test.strelka.variants.TsTv.qual has different md5sums on my linux system and the GitHub-test-server.
# I don't know exactly why that is, but the file contains some very small numbers written in scientific notation 4.00193e-322 which might change slightly on different systems.
# Instead I'll try some string testing
contains: ["0 0 0 -nan 3 4 0.75", "2 0 1 0 2 4 0.5", "5 1 1 1 2 3 0.666667"]
- path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
# binary changes md5sums on reruns.
- path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
# binary changes md5sums on reruns.
- path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
# binary changes md5sums on reruns.
- path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
# binary changes md5sums on reruns.
- path: results/csv/recalibrated.csv
should_exist: false
- path: results/preprocessing/markduplicates/test/test.md.cram
should_exist: false
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
should_exist: false
- path: results/preprocessing/recal_table/test/test.recal.table
should_exist: false
- path: results/preprocessing/recalibrated/test/test.recal.cram
should_exist: false
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
should_exist: false
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
should_exist: false
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
should_exist: false
- path: results/reports/samtools/test/test.recal.cram.stats
should_exist: false
- path: results/preprocessing/mapped/
should_exist: false
- path: results/preprocessing/markduplicates/
should_exist: false