Skip to content
Snippets Groups Projects
Select Git revision
  • master default protected
  • dev
  • v2.0.0
  • v0.4.0
  • v0.3.0
  • v0.2.9
  • v0.2.8
  • v0.2.7
  • v0.2.6
  • v0.1.0
  • v0.2.5
  • v0.2.4
  • v0.2.3
  • v0.2.2
  • v0.2.1
  • v0.2.0
  • v0.1.2
17 results
Blame Permalink
tests.sh 1.53 KiB
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 






./nextflow src/nf_modules/samtools/sort_bams.nf \
  -c src/nf_modules/samtools/sort_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.bam" \
  -resume

./nextflow src/nf_modules/samtools/index_bams.nf \
  -c src/nf_modules/samtools/index_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
  -resume

./nextflow src/nf_modules/samtools/split_bams.nf \
  -c src/nf_modules/samtools/split_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.bam" \
  -resume

./nextflow src/nf_modules/samtools/filter_bams.nf \
  -c src/nf_modules/samtools/filter_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.bam" \
  --bed "data/tiny_dataset/OLD/2genes.bed" \
  -resume

if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/samtools/sort_bams.nf \
  -c src/nf_modules/samtools/sort_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.bam" \
  -resume

./nextflow src/nf_modules/samtools/index_bams.nf \
  -c src/nf_modules/samtools/index_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
  -resume

./nextflow src/nf_modules/samtools/split_bams.nf \
  -c src/nf_modules/samtools/split_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.bam" \
  -resume

./nextflow src/nf_modules/samtools/filter_bams.nf \
  -c src/nf_modules/samtools/filter_bams.config \
  -profile docker \
  --bam "data/tiny_dataset/map/tiny_v2.bam" \
  --bed "data/tiny_dataset/OLD/2genes.bed" \
  -resume
fi