mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
8d04c34934
* add ismapper module * Update main.nf * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
44 lines
1.5 KiB
Text
44 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process ISMAPPER {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1"
|
|
} else {
|
|
container "quay.io/biocontainers/ismapper:2.0.2--pyhdfd78af_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads), path(reference), path(query)
|
|
|
|
output:
|
|
tuple val(meta), path("results/*"), emit: results
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
ismap \\
|
|
$options.args \\
|
|
--t $task.cpus \\
|
|
--output_dir results \\
|
|
--queries $query \\
|
|
--reference $reference \\
|
|
--reads $reads
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$( echo \$( ismap --version 2>&1 ) | sed 's/^.*ismap //' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|