kkonganti@105: process FLYE_ASSEMBLE {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_medium'
kkonganti@105:     // errorStrategy 'ignore'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}flye${params.fs}2.8" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::flye=2.8.1" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/flye:2.8.1--py37h8270d21_1' :
kkonganti@105:         'quay.io/biocontainers/flye:2.8.1--py37h8270d21_1' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(reads)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     path "${meta.id}${params.fs}*"
kkonganti@105:     tuple val(meta), path("${meta.id}${params.fs}assembly.fasta"), emit: assembly, optional: true
kkonganti@105:     path "versions.yml"                                          , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     """
kkonganti@105:     reads_platform=\$( echo "$args" | grep -E -o '(--nano|--pacbio)-(raw|corr|hq|hifi)' )
kkonganti@105:     flye \\
kkonganti@105:         \$(echo "$args" | sed -e "s/\$reads_platform//") \\
kkonganti@105:         -t $task.cpus \\
kkonganti@105:         --out-dir "${meta.id}" \\
kkonganti@105:         \$reads_platform \\
kkonganti@105:         $reads
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         flye: \$( flye --version )
kkonganti@105:     END_VERSIONS
kkonganti@105: 
kkonganti@105:     grepver=""
kkonganti@105: 
kkonganti@105:     if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@105:         grepver=\$( grep --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@105:     else
kkonganti@105:         grepver=\$( echo \$( grep --version 2>&1 ) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
kkonganti@105:     fi
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS >> versions.yml
kkonganti@105:         grep: \$grepver
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }