millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-13 05:13:09 +00:00
Code Issues Releases Packages Activity

samtools mpileup now bgzips mpileup files

Browse source
This commit is contained in:
WackerO 2022-06-11 13:32:53 +02:00
parent afed00fb62
commit dc6c09e083
2 changed files with 6 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

3
modules/samtools/mpileup/main.nf
View file

@ -11,7 +11,7 @@ process SAMTOOLS_MPILEUP {
path fasta
output:
tuple val(meta), path("*.mpileup"), emit: mpileup
tuple val(meta), path("*.mpileup.gz"), emit: mpileup
path "versions.yml" , emit: versions
when:
@ -27,6 +27,7 @@ process SAMTOOLS_MPILEUP {
--output ${prefix}.mpileup \\
$args \\
$input
bgzip ${prefix}.mpileup
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

8
tests/modules/samtools/mpileup/test.yml
View file

@ -4,8 +4,8 @@
- samtools
- samtools/mpileup
files:
- path: output/samtools/test.mpileup
md5sum: 958e6bead4103d72026f80153b6b5150
- path: output/samtools/test.mpileup.gz
md5sum: 29455c36377196e8bc9cf831cf17b5dc
- path: output/samtools/versions.yml
- name: samtools mpileup test_samtools_mpileup_intervals
@ -14,6 +14,6 @@
- samtools
- samtools/mpileup
files:
- path: output/samtools/test.mpileup
md5sum: 958e6bead4103d72026f80153b6b5150
- path: output/samtools/test.mpileup.gz
md5sum: 29455c36377196e8bc9cf831cf17b5dc
- path: output/samtools/versions.yml