kkonganti@105: process KRAKEN2_EXTRACT_CONTIGS {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_nano'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@105:     conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
kkonganti@105:         'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(assembly), path(kraken2_output)
kkonganti@105:     val kraken2_extract_bug
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val(meta), path('*assembly_filtered_contigs.fasta'), emit: asm_filtered_contigs
kkonganti@105:     path "versions.yml"                                      , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     """
kkonganti@105:     extract_assembled_filtered_contigs.py \\
kkonganti@105:         -i $assembly \\
kkonganti@105:         -o ${prefix}.assembly_filtered_contigs.fasta \\
kkonganti@105:         -k $kraken2_output \\
kkonganti@105:         -b '$kraken2_extract_bug'
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         python: \$( python --version | sed 's/Python //g' )
kkonganti@105:         biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' )
kkonganti@105:         numpy: \$( python -c 'import numpy as np; print(np.__version__)' )
kkonganti@105:         pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' )
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }