nf-core_modules/modules/samtools/convert/main.nf

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process SAMTOOLS_CONVERT {
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:
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tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index
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path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
def output_extension = input.getExtension() == "bam" ? "cram" : "bam"
"""
samtools view \\
--threads ${task.cpus} \\
--reference ${fasta} \\
$args \\
$input \\
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-o ${prefix}.${output_extension}
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samtools index -@${task.cpus} ${prefix}.${output_extension}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}