mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
569e07f0af
* add new samtools/bamtocram module * fix md5sum * remove md5sum * Update modules/samtools/bamtocram/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
Text
//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
|
|
process SAMTOOLS_BAMTOCRAM {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
|
|
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input), path(index)
|
|
path fasta
|
|
path fai
|
|
|
|
output:
|
|
tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
|
|
samtools index -@${task.cpus} ${prefix}.cram
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|