Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.2/modules/kraken2/extract_contigs/main.nf @ 130:04f6ac8ca13c
planemo upload
| author | kkonganti |
|---|---|
| date | Wed, 03 Jul 2024 15:16:39 -0400 |
| parents | 52045ea4679d |
| children |
| rev | line source |
|---|---|
| kkonganti@105 | 1 process KRAKEN2_EXTRACT_CONTIGS { |
| kkonganti@105 | 2 tag "$meta.id" |
| kkonganti@105 | 3 label 'process_nano' |
| kkonganti@105 | 4 |
| kkonganti@105 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@105 | 6 conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null) |
| kkonganti@105 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@105 | 8 'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' : |
| kkonganti@105 | 9 'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }" |
| kkonganti@105 | 10 |
| kkonganti@105 | 11 input: |
| kkonganti@105 | 12 tuple val(meta), path(assembly), path(kraken2_output) |
| kkonganti@105 | 13 val kraken2_extract_bug |
| kkonganti@105 | 14 |
| kkonganti@105 | 15 output: |
| kkonganti@105 | 16 tuple val(meta), path('*assembly_filtered_contigs.fasta'), emit: asm_filtered_contigs |
| kkonganti@105 | 17 path "versions.yml" , emit: versions |
| kkonganti@105 | 18 |
| kkonganti@105 | 19 when: |
| kkonganti@105 | 20 task.ext.when == null || task.ext.when |
| kkonganti@105 | 21 |
| kkonganti@105 | 22 script: |
| kkonganti@105 | 23 def args = task.ext.args ?: '' |
| kkonganti@105 | 24 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@105 | 25 """ |
| kkonganti@105 | 26 extract_assembled_filtered_contigs.py \\ |
| kkonganti@105 | 27 -i $assembly \\ |
| kkonganti@105 | 28 -o ${prefix}.assembly_filtered_contigs.fasta \\ |
| kkonganti@105 | 29 -k $kraken2_output \\ |
| kkonganti@105 | 30 -b '$kraken2_extract_bug' |
| kkonganti@105 | 31 |
| kkonganti@105 | 32 cat <<-END_VERSIONS > versions.yml |
| kkonganti@105 | 33 "${task.process}": |
| kkonganti@105 | 34 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@105 | 35 biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' ) |
| kkonganti@105 | 36 numpy: \$( python -c 'import numpy as np; print(np.__version__)' ) |
| kkonganti@105 | 37 pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' ) |
| kkonganti@105 | 38 END_VERSIONS |
| kkonganti@105 | 39 """ |
| kkonganti@105 | 40 } |