mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
dce27b8102
* Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BLAST_BLASTN {
|
|
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::blast=2.10.1' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
|
|
} else {
|
|
container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
path db
|
|
|
|
output:
|
|
tuple val(meta), path('*.blastn.txt'), emit: txt
|
|
path '*.version.txt' , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
|
|
blastn \\
|
|
-num_threads $task.cpus \\
|
|
-db \$DB \\
|
|
-query $fasta \\
|
|
$options.args \\
|
|
-out ${prefix}.blastn.txt
|
|
echo \$(blastn -version 2>&1) | sed 's/^.*blastn: //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|