Mercurial > repos > kkonganti > cfsan_cronology

annotate 0.2.0/modules/index_pdg_metadata/main.nf @ 18:a72c172df773 tip

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 21:40:42 -0400
parents a5f31c44f8c9
children
rev   line source
kkonganti@11 1 process INDEX_PDG_METADATA {
kkonganti@11 2 tag "index_pdg_metadata.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 path pdg_metadata
kkonganti@11 13 path pdg_ref_snp_metadata
kkonganti@11 14 path accs_all
kkonganti@11 15 path mlst_results
kkonganti@11 16
kkonganti@11 17 output:
kkonganti@11 18 path "*.pickle" , emit: index
kkonganti@11 19 path 'versions.yml', emit: versions
kkonganti@11 20
kkonganti@11 21 when:
kkonganti@11 22 task.ext.when == null || task.ext.when
kkonganti@11 23
kkonganti@11 24 script:
kkonganti@11 25 def args = task.ext.args ?: ''
kkonganti@11 26 def mlst_results = (mlst_results ? "-mlst ${mlst_results}" : '')
kkonganti@11 27 """
kkonganti@11 28 index_pdg_metadata.py \\
kkonganti@11 29 $mlst_results \\
kkonganti@11 30 -pdg_dir "."
kkonganti@11 31
kkonganti@11 32 cat <<-END_VERSIONS > versions.yml
kkonganti@11 33 "${task.process}":
kkonganti@11 34 python: \$( python --version | sed 's/Python //g' )
kkonganti@11 35 END_VERSIONS
kkonganti@11 36 """
kkonganti@11 37
kkonganti@11 38 }