mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
2.2 KiB
Text
57 lines
2.2 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PBCCS {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
publishDir "${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::pbccs=6.0.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/pbccs:6.0.0--h9ee0642_2"
|
|
} else {
|
|
container "quay.io/biocontainers/pbccs:6.0.0--h9ee0642_2"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(pbi)
|
|
val chunk_num
|
|
val chunk_on
|
|
|
|
output:
|
|
tuple val(meta), path("*.ccs.bam") , emit: bam
|
|
tuple val(meta), path("*.ccs.bam.pbi") , emit: pbi
|
|
tuple val(meta), path("*.ccs_report.txt" ) , emit: ccs_report_txt
|
|
tuple val(meta), path("*.ccs_report.json" ) , emit: ccs_report_json
|
|
tuple val(meta), path("*.zmw_metrics.json.gz"), emit: zmw_metrics
|
|
tuple val(meta), path("versions.yml" ) , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
// def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def ccs = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs.bam'
|
|
def report_txt = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.txt'
|
|
def report_json = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.json'
|
|
def zmw_metrics = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.zmw_metrics.json.gz'
|
|
"""
|
|
ccs \\
|
|
$bam \\
|
|
$ccs \\
|
|
--report-file $report_txt \\
|
|
--report-json $report_json \\
|
|
--metrics-json $zmw_metrics \\
|
|
--chunk $chunk_num/$chunk_on \\
|
|
-j $task.cpus \\
|
|
$options.args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(ccs --version 2>&1 | grep -e 'commit')
|
|
END_VERSIONS
|
|
"""
|
|
}
|