kkonganti@11: process SCAFFOLD_GENOMES {
kkonganti@11:     tag "fasta_join.pl"
kkonganti@11:     label "process_micro"
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
kkonganti@11:     conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
kkonganti@11:         'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         path acc_chunk_file
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         val "${params.output}${params.fs}scaffold_genomes", emit: genomes_dir
kkonganti@11:         path '*_scaffolded_genomic.fna.gz'                , emit: scaffolded
kkonganti@11:         path 'versions.yml'                               , emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args = task.ext.args ?: ''
kkonganti@11:         """
kkonganti@11:         datasets download genome accession \\
kkonganti@11:             --dehydrated \\
kkonganti@11:             --inputfile $acc_chunk_file
kkonganti@11: 
kkonganti@11:         unzip ncbi_dataset.zip
kkonganti@11: 
kkonganti@11:         datasets rehydrate \\
kkonganti@11:             --gzip \\
kkonganti@11:             --max-workers $task.cpus \\
kkonganti@11:             --directory "."
kkonganti@11: 
kkonganti@11:         fasta_join.pl -in ncbi_dataset
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             datasets: \$( datasets --version | sed 's/datasets version: //g' )
kkonganti@11:             perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
kkonganti@11:             bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
kkonganti@11:         END_VERSIONS
kkonganti@11: 
kkonganti@11:         zcmd=""
kkonganti@11:         zver=""
kkonganti@11: 
kkonganti@11:         if type pigz > /dev/null 2>&1; then
kkonganti@11:             zcmd="pigz"
kkonganti@11:             zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@11:         elif type gzip > /dev/null 2>&1; then
kkonganti@11:             zcmd="gzip"
kkonganti@11:         
kkonganti@11:             if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@11:                 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@11:             else
kkonganti@11:                 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@11:             fi
kkonganti@11:         fi
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS >> versions.yml
kkonganti@11:             \$zcmd: \$zver
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }