mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e8b33e6eb1
* hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added genomecov scale module * Updated tagging * Removed extra module - began merging * Removed extra module tests * Updated genomecov to take a scale value * Updated line endings * Removed redundant test * Update tests/modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added checking for existing -bg arg * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
68 lines
2.2 KiB
Text
68 lines
2.2 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BEDTOOLS_GENOMECOV {
|
|
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::bedtools=2.30.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
|
} else {
|
|
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(intervals), val(scale)
|
|
path sizes
|
|
val extension
|
|
|
|
output:
|
|
tuple val(meta), path("*.${extension}"), emit: genomecov
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def args_token = options.args.tokenize()
|
|
def args = options.args
|
|
args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
|
|
|
|
if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
|
|
args += " -bg"
|
|
}
|
|
|
|
if (intervals.name =~ /\.bam/) {
|
|
"""
|
|
bedtools \\
|
|
genomecov \\
|
|
-ibam $intervals \\
|
|
$args \\
|
|
> ${prefix}.${extension}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
|
END_VERSIONS
|
|
"""
|
|
} else {
|
|
"""
|
|
bedtools \\
|
|
genomecov \\
|
|
-i $intervals \\
|
|
-g $sizes \\
|
|
$args \\
|
|
> ${prefix}.${extension}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
|
|
END_VERSIONS
|
|
"""
|
|
}
|
|
}
|