Mercurial > repos > kkonganti > cfsan_bettercallsal
comparison 0.5.0/modules/index_metadata/main.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
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| 0:a4b1ee4b68b1 | 1:365849f031fd |
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| 1 process INDEX_METADATA { | |
| 2 tag "get_top_unique_mash_hit_genomes.py" | |
| 3 label "process_pico" | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) | |
| 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : | |
| 9 'quay.io/biocontainers/python:3.10.4' }" | |
| 10 | |
| 11 input: | |
| 12 tuple val(type), path(sero_tbl) | |
| 13 | |
| 14 output: | |
| 15 path '*.ACC2SERO.pickle', emit: acc2sero | |
| 16 path 'versions.yml' , emit: versions | |
| 17 | |
| 18 when: | |
| 19 task.ext.when == null || task.ext.when | |
| 20 | |
| 21 script: | |
| 22 def args = task.ext.args ?: '' | |
| 23 def prefix = ( | |
| 24 type.find(/_comp/) \ | |
| 25 ? type.replaceAll(/\_comp/, 'per_comp_serotype') \ | |
| 26 : type.replaceAll(/\_snp/, 'per_snp_cluster') | |
| 27 ) | |
| 28 """ | |
| 29 get_top_unique_mash_hit_genomes.py \\ | |
| 30 -s $sero_tbl -op $prefix | |
| 31 | |
| 32 cat <<-END_VERSIONS > versions.yml | |
| 33 "${task.process}": | |
| 34 python: \$( python --version | sed 's/Python //g' ) | |
| 35 END_VERSIONS | |
| 36 """ | |
| 37 } |