nf-core_modules/modules/diamond/blastp/main.nf
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* 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>
2021-09-27 09:41:24 +01:00

50 lines
1.7 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process DIAMOND_BLASTP {
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']) }
// Dimaond is limited to v2.0.9 because there is not a
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0'
} else {
container "quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0"
}
input:
tuple val(meta), path(fasta)
path db
output:
tuple val(meta), path('*.txt'), emit: txt
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
diamond \\
blastp \\
--threads $task.cpus \\
--db \$DB \\
--query $fasta \\
$options.args \\
--out ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
END_VERSIONS
"""
}