--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/gunc/run/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,80 @@
+process GUNC_RUN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}gunc${params.fs}1.0.5" : null)
+    conda (params.enable_conda ? "conda-forge::pandas=1.5.1 bioconda::gunc=1.0.5" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
+        'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
+
+    input:
+        tuple val(meta), path(database_path), path(fasta_ford, stageAs: 'fasta_ford.txt')
+
+    output:
+        tuple val(meta), path("**${params.fs}*maxCSS_level.tsv")        , emit: maxcss_level_tsv
+        tuple val(meta), path("**${params.fs}*all_levels.tsv")          , emit: all_levels_tsv, optional: true
+        tuple val(meta), path("**${params.fs}*.maxCSS_level.passed.tsv"), emit: quality_report_passed 
+        path "versions.yml"                                             , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args        = task.ext.args ?: ''
+        def prefix      = task.ext.prefix ?: "${meta.id}"
+        def outdir      = prefix + (task.index ?: '')
+        def input       = "${fasta_ford}"
+        def fgq_py_args = []
+        fgq_py_args.addAll([
+            ("${params.fgq_py_gunc_extract}" ? "-extract ${params.fgq_py_gunc_extract}" : "-extract genome"),
+            ("${params.fgq_py_gunc_fcn}" ? "-fcn ${params.fgq_py_gunc_fcn}" : "-fcn 'clade_separation_score,contamination_portion'"),
+            ("${params.fgq_py_gunc_fcv}" ? "-fcv ${params.fgq_py_gunc_fcv}" : "-fcv '0.05,0.05'"),
+            ("${params.fgq_py_gunc_conds}" ? "-conds ${params.fgq_py_gunc_conds}" : "-conds '<=,<='")
+        ])
+        if (params.guncrun_in_is_dir) {
+            input = "--input_dir ${fasta_ford}"
+        } else if (params.guncrun_in_is_fofn) {
+            input = "--input_file ${fasta_ford}"
+        } else if (params.guncrun_in_is_fasta) {
+            input = "--input_fasta ${fasta_ford}"
+        } else {
+            input = "--input_dir unscaffolded"
+        }
+        """
+        mkdir -p $outdir || exit 1
+
+        datasets download genome accession \\
+            --dehydrated \\
+            --inputfile $fasta_ford
+
+        unzip ncbi_dataset.zip
+
+        datasets rehydrate \\
+            --gzip \\
+            --max-workers $task.cpus \\
+            --directory "."
+
+        stage_ncbi_dataset_genomes.py -in ncbi_dataset
+
+        gunc \\
+            run \\
+            --db_file $database_path \\
+            --threads $task.cpus \\
+            --out_dir $outdir \\
+            $input \\
+            $args
+
+        filter_genomes_by_qual.py \\
+            -tsv $outdir${params.fs}GUNC.progenomes_2.1.maxCSS_level.tsv \\
+            -outprefix "${outdir}_" \\
+            ${fgq_py_args.join(' ')}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            datasets: \$( datasets --version | sed 's/datasets version: //g' )
+            python: \$( python --version | sed 's/Python //g' )
+            gunc: \$( gunc --version )
+        END_VERSIONS
+        """
+}
\ No newline at end of file