--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/kraken2/extract_contigs/main.nf	Thu Jun 27 14:17:26 2024 -0400
@@ -0,0 +1,40 @@
+process KRAKEN2_EXTRACT_CONTIGS {
+    tag "$meta.id"
+    label 'process_nano'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
+        'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }"
+
+    input:
+    tuple val(meta), path(assembly), path(kraken2_output)
+    val kraken2_extract_bug
+
+    output:
+    tuple val(meta), path('*assembly_filtered_contigs.fasta'), emit: asm_filtered_contigs
+    path "versions.yml"                                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    extract_assembled_filtered_contigs.py \\
+        -i $assembly \\
+        -o ${prefix}.assembly_filtered_contigs.fasta \\
+        -k $kraken2_output \\
+        -b '$kraken2_extract_bug'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$( python --version | sed 's/Python //g' )
+        biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' )
+        numpy: \$( python -c 'import numpy as np; print(np.__version__)' )
+        pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' )
+    END_VERSIONS
+    """
+}
\ No newline at end of file