nf-core_modules/modules/bcftools/reheader/main.nf
Johnathan D a813e2e3a6
Add bcftools reheader (#585) (#608)
* local tests and linting passing (#585)

* fix: picard filtersamreads input (#610)

* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Added module arriba (#611)

* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* added test for new header

* enhance module fastp: add `save_merged` (#598) (#614)

* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-23 22:24:19 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BCFTOOLS_REHEADER {
tag "$meta.id"
label 'process_low'
publishDir "${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']) }
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
} else {
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
}
input:
tuple val(meta), path(vcf)
path fai
path header
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def update_sequences = fai ? "-f $fai" : ""
def new_header = header ? "-h $header" : ""
"""
bcftools \\
reheader \\
$update_sequences \\
$new_header \\
$options.args \\
--threads $task.cpus \\
-o ${prefix}.vcf.gz \\
$vcf
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
"""
}