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

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Text

def VERSION = '0.1.1'
process HMMCOPY_GENERATEMAP {
tag '$bam'
label 'process_long'
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
input:
path fasta
output:
path "*.map.bw" , emit: bigwig
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
# build required indexes
generateMap.pl -b \\
$args \\
$fasta
# run
generateMap.pl \\
$args \\
$fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
hmmcopy: \$(echo $VERSION)
END_VERSIONS
"""
}