kkonganti@1: process SCAFFOLD_GENOMES {
kkonganti@1:     tag "fasta_join.pl"
kkonganti@1:     label "process_nano"
kkonganti@1: 
kkonganti@1:     module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
kkonganti@1:     conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
kkonganti@1:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@1:         'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
kkonganti@1:         'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
kkonganti@1: 
kkonganti@1:     input:
kkonganti@1:         path acc_chunk_file
kkonganti@1: 
kkonganti@1:     output:
kkonganti@1:         val "${params.output}${params.fs}scaffold_genomes", emit: genomes_dir
kkonganti@1:         path '*_scaffolded_genomic.fna.gz'                , emit: scaffolded
kkonganti@1:         path 'versions.yml'                               , emit: versions
kkonganti@1: 
kkonganti@1:     when:
kkonganti@1:         task.ext.when == null || task.ext.when
kkonganti@1: 
kkonganti@1:     script:
kkonganti@1:         def args = task.ext.args ?: ''
kkonganti@1:         """
kkonganti@1:         datasets download genome accession \\
kkonganti@1:             --dehydrated \\
kkonganti@1:             --inputfile $acc_chunk_file
kkonganti@1: 
kkonganti@1:         unzip ncbi_dataset.zip
kkonganti@1: 
kkonganti@1:         datasets rehydrate \\
kkonganti@1:             --gzip \\
kkonganti@1:             --directory "."
kkonganti@1: 
kkonganti@1:         fasta_join.pl -in ncbi_dataset
kkonganti@1: 
kkonganti@1:         cat <<-END_VERSIONS > versions.yml
kkonganti@1:         "${task.process}":
kkonganti@1:             datasets: \$( datasets --version | sed 's/datasets version: //g' )
kkonganti@1:             perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
kkonganti@1:             bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
kkonganti@1:         END_VERSIONS
kkonganti@1: 
kkonganti@1:         zcmd=""
kkonganti@1:         zver=""
kkonganti@1: 
kkonganti@1:         if type pigz > /dev/null 2>&1; then
kkonganti@1:             zcmd="pigz"
kkonganti@1:             zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@1:         elif type gzip > /dev/null 2>&1; then
kkonganti@1:             zcmd="gzip"
kkonganti@1:         
kkonganti@1:             if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@1:                 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@1:             else
kkonganti@1:                 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@1:             fi
kkonganti@1:         fi
kkonganti@1: 
kkonganti@1:         cat <<-END_VERSIONS >> versions.yml
kkonganti@1:             \$zcmd: \$zver
kkonganti@1:         END_VERSIONS
kkonganti@1:         """
kkonganti@1: }