process BLAST_BLASTN { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : '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 "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'` blastn \\ -num_threads $task.cpus \\ -db \$DB \\ -query $fasta \\ $args \\ -out ${prefix}.blastn.txt cat <<-END_VERSIONS > versions.yml "${task.process}": blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//') END_VERSIONS """ }