kkonganti@105: process SEQSERO2 {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_low'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}seqsero2${params.fs}1.2.1" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' :
kkonganti@105:         'quay.io/biocontainers/seqsero2:1.2.1--py_0' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(reads_or_asm)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     path("${meta.id}${params.fs}*")
kkonganti@105:     tuple val(meta), path("${meta.id}${params.fs}*_result.tsv"), emit: serotyped
kkonganti@105:     path "versions.yml"                                        , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     (task.ext.when == null || task.ext.when) && reads_or_asm.size() > 0
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     """
kkonganti@105:     SeqSero2_package.py \\
kkonganti@105:         $args \\
kkonganti@105:         -d $prefix \\
kkonganti@105:         -n $prefix \\
kkonganti@105:         -p $task.cpus \\
kkonganti@105:         -i $reads_or_asm
kkonganti@105: 
kkonganti@105:     mv ${prefix}${params.fs}SeqSero_log.txt ${prefix}${params.fs}${prefix}.SeqSero_log.txt
kkonganti@105:     mv ${prefix}${params.fs}SeqSero_result.txt ${prefix}${params.fs}${prefix}.SeqSero_result.txt
kkonganti@105:     mv ${prefix}${params.fs}SeqSero_result.tsv ${prefix}${params.fs}${prefix}.SeqSero_result.tsv
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' )
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }