nf-core_modules/modules/ivar/consensus/main.nf

50 lines
1.7 KiB
Text
Raw Normal View History

2021-02-09 18:26:35 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
2021-02-09 18:26:35 +00:00
params.options = [:]
options = initOptions(params.options)
2021-02-09 18:26:35 +00:00
process IVAR_CONSENSUS {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
2021-02-09 18:26:35 +00:00
conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
2021-02-09 18:26:35 +00:00
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
} else {
container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
}
input:
tuple val(meta), path(bam)
2021-02-12 23:01:53 +00:00
path fasta
2021-02-09 18:26:35 +00:00
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
2021-02-09 18:26:35 +00:00
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
2021-02-09 18:26:35 +00:00
"""
samtools mpileup \\
2021-02-23 20:36:03 +00:00
--reference $fasta \\
2021-02-09 18:26:35 +00:00
$options.args2 \\
$bam | \\
$save_mpileup \\
2021-02-09 18:26:35 +00:00
ivar consensus \\
2021-02-12 22:57:06 +00:00
$options.args \\
-p $prefix
2021-02-09 18:26:35 +00:00
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
2021-02-09 18:26:35 +00:00
"""
}