kkonganti@17: process SCAFFOLD_GENOMES {
kkonganti@17:     tag "fasta_join.pl"
kkonganti@17:     label "process_nano"
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
kkonganti@17:         'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         path acc_chunk_file
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         val "${params.output}${params.fs}scaffold_genomes", emit: genomes_dir
kkonganti@17:         path '*_scaffolded_genomic.fna.gz'                , emit: scaffolded
kkonganti@17:         path 'versions.yml'                               , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         """
kkonganti@17:         datasets download genome accession \\
kkonganti@17:             --dehydrated \\
kkonganti@17:             --inputfile $acc_chunk_file
kkonganti@17: 
kkonganti@17:         unzip ncbi_dataset.zip
kkonganti@17: 
kkonganti@17:         datasets rehydrate \\
kkonganti@17:             --gzip \\
kkonganti@17:             --max-workers $task.cpus \\
kkonganti@17:             --directory "."
kkonganti@17: 
kkonganti@17:         fasta_join.pl -in ncbi_dataset
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             datasets: \$( datasets --version | sed 's/datasets version: //g' )
kkonganti@17:             perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
kkonganti@17:             bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
kkonganti@17:         END_VERSIONS
kkonganti@17: 
kkonganti@17:         zcmd=""
kkonganti@17:         zver=""
kkonganti@17: 
kkonganti@17:         if type pigz > /dev/null 2>&1; then
kkonganti@17:             zcmd="pigz"
kkonganti@17:             zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@17:         elif type gzip > /dev/null 2>&1; then
kkonganti@17:             zcmd="gzip"
kkonganti@17:         
kkonganti@17:             if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@17:                 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@17:             else
kkonganti@17:                 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@17:             fi
kkonganti@17:         fi
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS >> versions.yml
kkonganti@17:             \$zcmd: \$zver
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }