--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/checkm2/predict/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,67 @@
+process CHECKM2_PREDICT {
+    tag "$meta.id"
+    label 'process_low'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}checkm2${params.fs}1.0.1" : null)
+    conda (params.enable_conda ? "conda-forge::scipy bioconda::checkm2=1.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/checkm2:1.0.1--pyh7cba7a3_0' :
+        'quay.io/biocontainers/checkm2:1.0.1--pyh7cba7a3_0+' }"
+
+    input:
+        tuple val(meta), path(database_path), path(acc_chunk_file, stageAs: 'acc_chunk_file.txt')
+
+    output:
+        tuple val(meta), path("**${params.fs}*quality_report.tsv")       , emit: quality_report
+        tuple val(meta), path("**${params.fs}*quality_report.passed.tsv"), emit: quality_report_passed
+        path "versions.yml"                                              , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args          = task.ext.args ?: ''
+        def prefix        = task.ext.prefix ?: "${meta.id}"
+        def outdir        = prefix + (task.index ?: '')
+        def fgq_py_args   = []
+        fgq_py_args.addAll([
+            ("${params.fgq_py_cm2_extract}" ? "-extract ${params.fgq_py_cm2_extract}" : "-extract Name"),
+            ("${params.fgq_py_cm2_fcn}" ? "-fcn ${params.fgq_py_cm2_fcn}" : "-fcn 'Completeness_General,Contamination,Completeness_Specific'"),
+            ("${params.fgq_py_cm2_fcv}" ? "-fcv ${params.fgq_py_cm2_fcv}" : "-fcv '97.5,1,99'"),
+            ("${params.fgq_py_cm2_conds}" ? "-conds ${params.fgq_py_cm2_conds}" : "-conds '>=,<=,>='")
+        ]) 
+        """
+        datasets download genome accession \\
+            --dehydrated \\
+            --inputfile $acc_chunk_file
+
+        unzip ncbi_dataset.zip
+
+        datasets rehydrate \\
+            --gzip \\
+            --max-workers $task.cpus \\
+            --directory "."
+
+        stage_ncbi_dataset_genomes.py -in ncbi_dataset
+
+        checkm2 \\
+            predict \\
+            --threads ${task.cpus} \\
+            --database_path $database_path \\
+            --input unscaffolded \\
+            --output_directory $outdir \\
+            $args
+
+        filter_genomes_by_qual.py \\
+            -tsv $outdir${params.fs}quality_report.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' )
+            checkm2: \$( checkm2 --version )
+        END_VERSIONS
+        """
+}
\ No newline at end of file