kkonganti@11: process GUNC_RUN {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label 'process_medium'
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}gunc${params.fs}1.0.5" : null)
kkonganti@11:     conda (params.enable_conda ? "conda-forge::pandas=1.5.1 bioconda::gunc=1.0.5" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
kkonganti@11:         'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(database_path), path(fasta_ford, stageAs: 'fasta_ford.txt')
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path("**${params.fs}*maxCSS_level.tsv")        , emit: maxcss_level_tsv
kkonganti@11:         tuple val(meta), path("**${params.fs}*all_levels.tsv")          , emit: all_levels_tsv, optional: true
kkonganti@11:         tuple val(meta), path("**${params.fs}*.maxCSS_level.passed.tsv"), emit: quality_report_passed 
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:         def prefix      = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         def outdir      = prefix + (task.index ?: '')
kkonganti@11:         def input       = "${fasta_ford}"
kkonganti@11:         def fgq_py_args = []
kkonganti@11:         fgq_py_args.addAll([
kkonganti@11:             ("${params.fgq_py_gunc_extract}" ? "-extract ${params.fgq_py_gunc_extract}" : "-extract genome"),
kkonganti@11:             ("${params.fgq_py_gunc_fcn}" ? "-fcn ${params.fgq_py_gunc_fcn}" : "-fcn 'clade_separation_score,contamination_portion'"),
kkonganti@11:             ("${params.fgq_py_gunc_fcv}" ? "-fcv ${params.fgq_py_gunc_fcv}" : "-fcv '0.05,0.05'"),
kkonganti@11:             ("${params.fgq_py_gunc_conds}" ? "-conds ${params.fgq_py_gunc_conds}" : "-conds '<=,<='")
kkonganti@11:         ])
kkonganti@11:         if (params.guncrun_in_is_dir) {
kkonganti@11:             input = "--input_dir ${fasta_ford}"
kkonganti@11:         } else if (params.guncrun_in_is_fofn) {
kkonganti@11:             input = "--input_file ${fasta_ford}"
kkonganti@11:         } else if (params.guncrun_in_is_fasta) {
kkonganti@11:             input = "--input_fasta ${fasta_ford}"
kkonganti@11:         } else {
kkonganti@11:             input = "--input_dir unscaffolded"
kkonganti@11:         }
kkonganti@11:         """
kkonganti@11:         mkdir -p $outdir || exit 1
kkonganti@11: 
kkonganti@11:         datasets download genome accession \\
kkonganti@11:             --dehydrated \\
kkonganti@11:             --inputfile $fasta_ford
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:         stage_ncbi_dataset_genomes.py -in ncbi_dataset
kkonganti@11: 
kkonganti@11:         gunc \\
kkonganti@11:             run \\
kkonganti@11:             --db_file $database_path \\
kkonganti@11:             --threads $task.cpus \\
kkonganti@11:             --out_dir $outdir \\
kkonganti@11:             $input \\
kkonganti@11:             $args
kkonganti@11: 
kkonganti@11:         filter_genomes_by_qual.py \\
kkonganti@11:             -tsv $outdir${params.fs}GUNC.progenomes_2.1.maxCSS_level.tsv \\
kkonganti@11:             -outprefix "${outdir}_" \\
kkonganti@11:             ${fgq_py_args.join(' ')}
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             datasets: \$( datasets --version | sed 's/datasets version: //g' )
kkonganti@11:             python: \$( python --version | sed 's/Python //g' )
kkonganti@11:             gunc: \$( gunc --version )
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }