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 output: tuple val(meta), path('*.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 "*.dmnd" | sed 's/.dmnd//'` diamond \\ blastp \\ --threads $task.cpus \\ --db \$DB \\ --query $fasta \\ $args \\ --out ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diamond: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //') END_VERSIONS """ }