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main.nf
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main.nf
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process SAMTOOLS_STATS {
tag "$meta.id"
label 'process_single'
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
'biocontainers/samtools:1.20--h50ea8bc_0' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta2), path(fasta)
output:
tuple val(meta), path("*.stats"), emit: stats
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--reference ${fasta}" : ""
"""
samtools \\
stats \\
--threads ${task.cpus} \\
${reference} \\
${input} \\
> ${prefix}.stats
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.stats
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}