kkonganti@105: process AMRFINDERPLUS_RUN {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_low'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}amrfinderplus${params.fs}3.10.24" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.24 conda-forge::libgcc-ng" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
kkonganti@105:         'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(fasta)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val(meta), path("${prefix}.tsv")          , emit: report
kkonganti@105:     tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
kkonganti@105:     path "versions.yml"                             , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     (task.ext.when == null || task.ext.when) && fasta.size() > 0
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def is_compressed = fasta.getName().endsWith(".gz") ? true : false
kkonganti@105:     prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
kkonganti@105:     fasta_name = fasta.getName().replace(".gz", "")
kkonganti@105:     fasta_param = "-n"
kkonganti@105:     if (meta.containsKey("is_proteins")) {
kkonganti@105:         if (meta.is_proteins) {
kkonganti@105:             fasta_param = "-p"
kkonganti@105:         }
kkonganti@105:     }
kkonganti@105:     """
kkonganti@105:     if [ "$is_compressed" == "true" ]; then
kkonganti@105:         gzip -c -d $fasta > $fasta_name
kkonganti@105:     fi
kkonganti@105: 
kkonganti@105:     amrfinder \\
kkonganti@105:         $fasta_param $fasta_name \\
kkonganti@105:         $organism_param \\
kkonganti@105:         $args \\
kkonganti@105:         --threads $task.cpus > ${prefix}.tsv
kkonganti@105: 
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         amrfinderplus: \$(amrfinder --version)
kkonganti@105:         gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' )
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }