Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/modules/index_metadata/main.nf @ 11:749faef1caa9
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 05 Sep 2023 11:51:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process INDEX_METADATA { |
| kkonganti@11 | 2 tag "get_top_unique_mash_hit_genomes.py" |
| kkonganti@11 | 3 label "process_pico" |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : |
| kkonganti@11 | 9 'quay.io/biocontainers/python:3.10.4' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(type), path(sero_tbl) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 path '*.ACC2SERO.pickle', emit: acc2sero |
| kkonganti@11 | 16 path 'versions.yml' , emit: versions |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 when: |
| kkonganti@11 | 19 task.ext.when == null || task.ext.when |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 script: |
| kkonganti@11 | 22 def args = task.ext.args ?: '' |
| kkonganti@11 | 23 def prefix = ( |
| kkonganti@11 | 24 type.find(/_comp/) \ |
| kkonganti@11 | 25 ? type.replaceAll(/\_comp/, 'per_comp_serotype') \ |
| kkonganti@11 | 26 : type.replaceAll(/\_snp/, 'per_snp_cluster') |
| kkonganti@11 | 27 ) |
| kkonganti@11 | 28 """ |
| kkonganti@11 | 29 get_top_unique_mash_hit_genomes.py \\ |
| kkonganti@11 | 30 -s $sero_tbl -op $prefix |
| kkonganti@11 | 31 |
| kkonganti@11 | 32 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 33 "${task.process}": |
| kkonganti@11 | 34 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@11 | 35 END_VERSIONS |
| kkonganti@11 | 36 """ |
| kkonganti@11 | 37 } |