mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
527ccdb419
* add racon * add miniasm module * edit miniasm module * edit miniasm module * Update tests/modules/racon/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update tests/modules/racon/test.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/miniasm/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update main.nf Add some spaces. * Update meta.yml Correct DOI * Update main.nf * Apply suggestions from code review * Update tests/modules/miniasm/test.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process MINIASM {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
publishDir "${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::miniasm=0.3_r179" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2"
|
|
} else {
|
|
container "quay.io/biocontainers/miniasm:0.3_r179--h5bf99c6_2"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads), path(paf)
|
|
|
|
output:
|
|
tuple val(meta), path("*.gfa.gz") , emit: gfa
|
|
tuple val(meta), path("*.fasta.gz"), emit: assembly
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
miniasm \\
|
|
$options.args \\
|
|
-f $reads \\
|
|
$paf > \\
|
|
${prefix}.gfa
|
|
|
|
awk '/^S/{print ">"\$2"\\n"\$3}' "${prefix}.gfa" | fold > ${prefix}.fasta
|
|
|
|
gzip -n ${prefix}.gfa
|
|
gzip -n ${prefix}.fasta
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$( miniasm -V 2>&1 )
|
|
END_VERSIONS
|
|
"""
|
|
}
|