mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
6d6e3a018f
* add module for mykrobe predict and genotyphi parse * Update meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
process MYKROBE_PREDICT {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1':
|
|
'quay.io/biocontainers/mykrobe:0.11.0--py39h2add14b_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(seqs)
|
|
val species
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}.csv") , emit: csv
|
|
tuple val(meta), path("${prefix}.json"), emit: json
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
mykrobe \\
|
|
predict \\
|
|
$args \\
|
|
--species $species \\
|
|
--threads $task.cpus \\
|
|
--sample $prefix \\
|
|
--format json_and_csv \\
|
|
--output ${prefix} \\
|
|
--seq $seqs
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
mykrobe: \$(echo \$(mykrobe --version 2>&1) | sed 's/^.*mykrobe v//' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|