nf-core_modules/modules/blast/blastn/main.nf
Harshil Patel c5235a983d
nf-core modules bump-versions for all modules (#630)
* Add blacklist of modules that shouldn't be updated to .nf-core.yml

* nf-core modules bump-versions for all modules

* Remove TODO statements identified by linting

* Fix md5sums for failing tests

* Fix more tests
2021-07-28 09:10:44 +01:00

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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=2.12.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
} else {
container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
}
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
"""
}