process DIAMOND_BLASTX { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" input: tuple val(meta), path(fasta) path db val out_ext val blast_columns output: tuple val(meta), path('*.blast'), optional: true, emit: blast tuple val(meta), path('*.xml') , optional: true, emit: xml tuple val(meta), path('*.txt') , optional: true, emit: txt tuple val(meta), path('*.daa') , optional: true, emit: daa tuple val(meta), path('*.sam') , optional: true, emit: sam tuple val(meta), path('*.tsv') , optional: true, emit: tsv tuple val(meta), path('*.paf') , optional: true, emit: paf tuple val(meta), path("*.log") , emit: log path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def columns = blast_columns ? "${blast_columns}" : '' switch ( out_ext ) { 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 default: outfmt = '6'; out_ext = 'txt'; log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)"); break } """ DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` diamond \\ blastx \\ --threads $task.cpus \\ --db \$DB \\ --query $fasta \\ --outfmt ${outfmt} ${columns} \\ $args \\ --out ${prefix}.${out_ext} \\ --log mv diamond.log ${prefix}.log cat <<-END_VERSIONS > versions.yml "${task.process}": diamond: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //') END_VERSIONS """ }