mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
bb90e4fb78
* Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process IVAR_CONSENSUS {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' :
|
|
'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
path fasta
|
|
val save_mpileup
|
|
|
|
output:
|
|
tuple val(meta), path("*.fa") , emit: fasta
|
|
tuple val(meta), path("*.qual.txt"), emit: qual
|
|
tuple val(meta), path("*.mpileup") , optional:true, emit: mpileup
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def args2 = task.ext.args2 ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
|
|
"""
|
|
samtools \\
|
|
mpileup \\
|
|
--reference $fasta \\
|
|
$args2 \\
|
|
$bam \\
|
|
$mpileup \\
|
|
| ivar \\
|
|
consensus \\
|
|
$args \\
|
|
-p $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|