Mercurial > repos > fubar > egapx_runner
view nf/subworkflows/ncbi/target_proteins/paf2asn/main.nf @ 8:1680e72e27be draft default tip
planemo upload for repository https://github.com/ncbi/egapx commit bdbe05027c2c40e217a2ff0c9e0556450c443e54
author | fubar |
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date | Mon, 05 Aug 2024 03:56:41 +0000 |
parents | d9c5c5b87fec |
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#!/usr/bin/env nextflow nextflow.enable.dsl=2 include { merge_params } from '../../utilities' workflow paf2asn { take: genome_asn_file //path: genome asn file proteins_asn_file //path: protein asn file paf_file //path: paf alignment file from miniprot parameters // Map : extra parameter and parameter update main: default_params = "" effective_params = merge_params(default_params, parameters, 'paf2asn') run_paf2asn(genome_asn_file, proteins_asn_file, paf_file, effective_params) emit: asn_file = run_paf2asn.out.asn_file } process run_paf2asn { label 'long_job' input: path genome, stageAs: 'LDS_Index/genome.asnt' path proteins, stageAs: 'LDS_Index/proteins.asnt' path paf_file // list of PAF files to convert val parameters output: path 'output/*.asn', emit: 'asn_file' script: def asn_name = paf_file.baseName.toString() + ".asn" """ mkdir -p output lds2_indexer -source LDS_Index echo "${paf_file.join('\n')}" > input.mft paf2asn ${parameters} -lds2 LDS_Index/lds2.db -nogenbank -input-manifest input.mft -o output/${asn_name} """ stub: def asn_name = paf_file.baseName.toString() + ".asn" """ mkdir -p output touch output/${asn_name} """ }