-
Notifications
You must be signed in to change notification settings - Fork 3
94 lines (84 loc) · 4.8 KB
/
main.yaml
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
name: tests
on:
push:
branches:
- master
- main
- unified
pull_request:
branches-ignore: []
jobs:
Dry_Run_and_Lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: docker://snakemake/snakemake:v6.8.2
- name: Tumor-normal FastQ Dry Run
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
/opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
/opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \
--output /opt2/output_tn_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
/opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
/opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \
--output /opt2/output_tn_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun
- name: Tumor-only FastQ Dry Run
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
/opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
/opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \
--output /opt2/output_tonly_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--genome hg38 --mode local --ffpe --runmode init
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
/opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
/opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.R2.fastq.gz \
--output /opt2/output_tonly_fqs --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--genome hg38 --mode local --ffpe --runmode dryrun
- name: Tumor-normal BAM Dry Run
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.recal.bam \
/opt2/.tests/Sample11_ACI_158_S38.recal.bam \
/opt2/.tests/Sample4_CRL1622_S31.recal.bam \
--output /opt2/output_tn_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.recal.bam \
/opt2/.tests/Sample11_ACI_158_S38.recal.bam \
/opt2/.tests/Sample4_CRL1622_S31.recal.bam \
--output /opt2/output_tn_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun
- name: Tumor-only BAM Dry Run
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.recal.bam \
/opt2/.tests/Sample11_ACI_158_S38.recal.bam \
/opt2/.tests/Sample4_CRL1622_S31.recal.bam \
--output /opt2/output_tonly_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--genome hg38 --mode local --ffpe --runmode init
docker run -v $PWD:/opt2 snakemake/snakemake:v6.8.2 \
/opt2/xavier run --input \
/opt2/.tests/Sample10_ARK1_S37.recal.bam \
/opt2/.tests/Sample11_ACI_158_S38.recal.bam \
/opt2/.tests/Sample4_CRL1622_S31.recal.bam \
--output /opt2/output_tonly_bams --targets /opt2/.tests/Agilent_SSv7_allExons_hg38.bed \
--genome hg38 --mode local --ffpe --runmode dryrun
- name: Lint Workflow
continue-on-error: true
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output_tn_fqs || \
echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'