kkonganti@105: process ABRICATE_RUN {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_low'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
kkonganti@105:         'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(assembly)
kkonganti@105:     val abdbs
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     path "${meta.id}${params.fs}*"
kkonganti@105:     tuple val(meta), path("${meta.id}${params.fs}*.ab.txt"), emit: abricated
kkonganti@105:     path "versions.yml"                                    , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     (task.ext.when == null || task.ext.when) && assembly.size() > 0
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     def dbs = abdbs.collect().join('\\n')
kkonganti@105:     """
kkonganti@105:     newprefix="${prefix}${params.fs}${prefix}"
kkonganti@105: 
kkonganti@105:     if [ ! -d "$prefix" ]; then
kkonganti@105:         mkdir "$prefix" || exit 1
kkonganti@105:     fi
kkonganti@105: 
kkonganti@105:     echo -e "$dbs" | while read -r db; do
kkonganti@105:         abricate \\
kkonganti@105:             $assembly \\
kkonganti@105:             $args \\
kkonganti@105:             --db \$db \\
kkonganti@105:             --threads $task.cpus 1> "\${newprefix}.\${db}.ab.txt"
kkonganti@105:     done
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
kkonganti@105:         bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }