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samtools mpileup now bgzips mpileup files

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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
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3
modules/samtools/mpileup/main.nf
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@ -11,7 +11,7 @@ process SAMTOOLS_MPILEUP {
path fasta path fasta
output: output:
tuple val(meta), path("*.mpileup"), emit: mpileup tuple val(meta), path("*.mpileup.gz"), emit: mpileup
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -27,6 +27,7 @@ process SAMTOOLS_MPILEUP {
--output ${prefix}.mpileup \\ --output ${prefix}.mpileup \\
$args \\ $args \\
$input $input
bgzip ${prefix}.mpileup
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') 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
- samtools/mpileup - samtools/mpileup
files: files:
- path: output/samtools/test.mpileup - path: output/samtools/test.mpileup.gz
md5sum: 958e6bead4103d72026f80153b6b5150 md5sum: 29455c36377196e8bc9cf831cf17b5dc
- path: output/samtools/versions.yml - path: output/samtools/versions.yml
- name: samtools mpileup test_samtools_mpileup_intervals - name: samtools mpileup test_samtools_mpileup_intervals
@ -14,6 +14,6 @@
- samtools - samtools
- samtools/mpileup - samtools/mpileup
files: files:
- path: output/samtools/test.mpileup - path: output/samtools/test.mpileup.gz
md5sum: 958e6bead4103d72026f80153b6b5150 md5sum: 29455c36377196e8bc9cf831cf17b5dc
- path: output/samtools/versions.yml - path: output/samtools/versions.yml