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26 lines
963 B
Text
26 lines
963 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf' addParams( options: [:] )
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include { GUNZIP } from '../../../../modules/gunzip/main.nf' addParams( options: [:] )
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include { GFFREAD } from '../../../../modules/gffread/main.nf' addParams( options: [args: "--sort-alpha --keep-genes -T", suffix: "_sorted"] )
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workflow test_ultra_pipeline {
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fastq = file(params.test_data['homo_sapiens']['pacbio']['hifi'] , checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'] , checkIfExists: true)
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genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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GUNZIP ( fastq )
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GFFREAD ( gtf )
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GUNZIP
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.out
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.gunzip
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.map { [ [ id:'test', single_end:false ], it ] }
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.set { input }
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ULTRA_PIPELINE ( input, genome, GFFREAD.out.gtf )
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}
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