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25 lines
866 B
Text
25 lines
866 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GUNZIP } from '../../../../modules/gunzip/main.nf'
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include { GFFREAD } from '../../../../modules/gffread/main.nf'
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include { ULTRA_INDEX } from '../../../../modules/ultra/index/main.nf'
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include { ULTRA_ALIGN } from '../../../../modules/ultra/align/main.nf'
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workflow test_ultra_align {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'] , checkIfExists: true)
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GUNZIP ( input )
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GFFREAD ( gtf )
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ULTRA_INDEX ( genome, GFFREAD.out.gtf )
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ULTRA_ALIGN ( GUNZIP.out.gunzip, genome, ULTRA_INDEX.out.index )
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}
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