nf-core_modules/modules/diamond/blastp/main.nf

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process DIAMOND_BLASTP {
tag "$meta.id"
label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
input:
tuple val(meta), path(fasta)
path db
val outext
output:
tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
switch ( outext ) {
case "blast": outfmt = 0; break
case "xml": outfmt = 5; break
case "txt": outfmt = 6; break
case "daa": outfmt = 100; break
case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break
}
"""
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
diamond \\
blastp \\
--threads $task.cpus \\
--db \$DB \\
--query $fasta \\
--outfmt ${outfmt} \\
$args \\
--out ${prefix}.${outext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diamond: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
END_VERSIONS
"""
}