nf-core_modules/software/ivar/trim/main.nf
Harshil Patel 9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml (#271)
* Rename pytest filters.yml

* Change filters.yml name

* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process IVAR_TRIM {
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), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
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), path(bai)
path bed
output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path('*.log'), emit: log
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
ivar trim \\
$options.args \\
-i $bam \\
-b $bed \\
-p $prefix \\
> ${prefix}.ivar.log
echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//' > ${software}.version.txt
"""
}