kkonganti@11: process DOWNLOAD_REF_GENOME {
kkonganti@11:     tag "${meta.id}"
kkonganti@11:     label "process_pico"
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@11:     conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@14:         'https://depot.galaxyproject.org/singularity/ncbi-datasets-pylib:15.31.1--pyhdfd78af_0' :
kkonganti@15:         'quay.io/biocontainers/python:3.10.4' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         val meta
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         path "*.fna"       , emit: fasta
kkonganti@11:         path "*.gff"       , emit: gff
kkonganti@11:         path 'versions.yml', emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args = task.ext.args ?: ''
kkonganti@11:         prefix   = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         """
kkonganti@14:         [ -e /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE=/usr/local/ssl/cacert.pem
kkonganti@14: 
kkonganti@11:         datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id}
kkonganti@11: 
kkonganti@11:         unzip ncbi_dataset.zip
kkonganti@11: 
kkonganti@11:         stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '_genomic.fna' -out "."
kkonganti@11: 
kkonganti@11:         stage_ncbi_dataset_genomes.py -in ncbi_dataset -suffix '.gff' -out "."
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             datasets: \$( datasets --version | sed 's/datasets version: //g' )
kkonganti@11:             python: \$( python --version | sed 's/Python //g' )
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: 
kkonganti@11: }