mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
ac1e6df076
* Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
41 lines
1.6 KiB
Text
41 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process SAMTOOLS_MERGE {
|
|
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::samtools=1.13' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
|
} else {
|
|
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(input_files)
|
|
path fasta
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}.bam"), optional:true, emit: bam
|
|
tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def file_type = input_files[0].getExtension()
|
|
def reference = fasta ? "--reference ${fasta}" : ""
|
|
"""
|
|
samtools merge ${reference} ${prefix}.${file_type} $input_files
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|