nf-core_modules/software/ivar/variants/main.nf
Anders Goncalves da Silva 4f8ab8bd69
Rename gff to features
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-15 19:53:30 -08:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process IVAR_VARIANTS {
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 fasta
path gff
output:
tuple val(meta), path("*.tsv") , emit: tsv
tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def save_mpileup = params.containsKey('save_mpileup') ? "tee ${prefix}.mpileup |" : ""
def gff = params.containsKey('gff') ? "-g ${params.get('gff')}" : ""
"""
samtools mpileup \\
$options.args2 \\
--reference $fasta \\
$bam | \\
$save_mpileup \\
ivar variants \\
$options.args \\
$features \\
-r $fasta \\
-p $prefix
ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
"""
}