Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.2/modules/kraken2/extract_contigs/main.nf @ 105:52045ea4679d

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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104:17890124001d 105:52045ea4679d
1 process KRAKEN2_EXTRACT_CONTIGS {
2 tag "$meta.id"
3 label 'process_nano'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
6 conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
9 'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }"
10
11 input:
12 tuple val(meta), path(assembly), path(kraken2_output)
13 val kraken2_extract_bug
14
15 output:
16 tuple val(meta), path('*assembly_filtered_contigs.fasta'), emit: asm_filtered_contigs
17 path "versions.yml" , emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 def prefix = task.ext.prefix ?: "${meta.id}"
25 """
26 extract_assembled_filtered_contigs.py \\
27 -i $assembly \\
28 -o ${prefix}.assembly_filtered_contigs.fasta \\
29 -k $kraken2_output \\
30 -b '$kraken2_extract_bug'
31
32 cat <<-END_VERSIONS > versions.yml
33 "${task.process}":
34 python: \$( python --version | sed 's/Python //g' )
35 biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' )
36 numpy: \$( python -c 'import numpy as np; print(np.__version__)' )
37 pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' )
38 END_VERSIONS
39 """
40 }