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Multithreaded samtools commands (#2080)

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* Multithreaded samtools commands

* Updated the checksums since the BAM files include the actual command line

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
This commit is contained in:
Matthieu Muffato 2022-09-26 17:44:36 +01:00 committed by GitHub
parent 1d668eefa2
commit f0a86eaf5b
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GPG key ID: 4AEE18F83AFDEB23
4 changed files with 9 additions and 6 deletions
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1
modules/samtools/ampliconclip/main.nf
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@ -31,6 +31,7 @@ process SAMTOOLS_AMPLICONCLIP {
"""
samtools \\
ampliconclip \\
--threads ${task.cpus-1} \\
$args \\
$rejects \\
$stats \\

1
modules/samtools/depth/main.nf
View file

@ -23,6 +23,7 @@ process SAMTOOLS_DEPTH {
"""
samtools \\
depth \\
--threads ${task.cpus-1} \\
$args \\
-o ${prefix}.tsv \\
$bam

1
modules/samtools/idxstats/main.nf
View file

@ -24,6 +24,7 @@ process SAMTOOLS_IDXSTATS {
"""
samtools \\
idxstats \\
--threads ${task.cpus-1} \\
$bam \\
> ${prefix}.idxstats

12
tests/modules/samtools/ampliconclip/test.yml
View file

@ -5,7 +5,7 @@
- samtools/ampliconclip
files:
- path: output/samtools/test.bam
md5sum: d270363a7fb3d96be2df211099efc75b
md5sum: 69e4ba713447864231f6cbbaf036c51d
- name: samtools ampliconclip no stats with rejects
command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@ -14,9 +14,9 @@
- samtools/ampliconclip
files:
- path: output/samtools/test.bam
md5sum: e7c4e64c259212e1670f6de96a5549b4
md5sum: dd2ed9d7cc4ddc070ece2dccc577f94b
- path: output/samtools/test.cliprejects.bam
md5sum: b7c057b11950c2271a0c92236bee94b7
md5sum: 7d641f6da838f41d75eaabbd897f60bd
- name: samtools ampliconclip with stats with rejects
command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@ -25,8 +25,8 @@
- samtools/ampliconclip
files:
- path: output/samtools/test.bam
md5sum: e75992d4ff69cbaed9a089231be86b5e
md5sum: 6c19afc0873fba2f4e530eabf61c0735
- path: output/samtools/test.cliprejects.bam
md5sum: 729f03e7a2801d2c56c32bef8f3d6ead
md5sum: 1dfb61aa80d8e90add324ed61ed17061
- path: output/samtools/test.clipstats.txt
md5sum: fc23355e1743d47f2541f2cb1a7a0cda
md5sum: 05ead360a98fab6a678056e326c4f1f3