nf-core_modules/modules/bbmap/index/main.nf
2022-02-04 09:53:32 +01:00

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process BBMAP_INDEX {
tag "$fasta"
label 'process_long'
conda (params.enable_conda ? "bioconda::bbmap=38.92" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' :
'quay.io/biocontainers/bbmap:38.92--he522d1c_0' }"
input:
path fasta
output:
path 'ref' , emit: index
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
bbmap.sh \\
ref=${fasta} \\
$args \\
threads=$task.cpus \\
-Xmx${task.memory.toGiga()}g
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bbmap: \$(bbversion.sh)
END_VERSIONS
"""
}