mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
38 lines
1 KiB
Text
38 lines
1 KiB
Text
|
process GAPPA_EXAMINEGRAFT {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_low'
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null)
|
||
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||
|
|
'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0':
|
||
|
|
'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }"
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(jplace)
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.newick"), emit: newick
|
||
|
|
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}"
|
||
|
|
"""
|
||
|
|
gappa \\
|
||
|
|
examine \\
|
||
|
|
graft \\
|
||
|
|
$args \\
|
||
|
|
--threads $task.cpus \\
|
||
|
|
--file-prefix ${prefix}. \\
|
||
|
|
--jplace-path $jplace
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|