mirror of
https://github.com/MillironX/nf-core_modules.git
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60c65fb386
* Add ultra/index and ultra/align modules * Correct tag and prefix * Fix typos * Remove SAMTOOLS SORT from test * Update: Convert sam to bam * Add tag to docker image * Fix typo * Add args2 for samtools
24 lines
866 B
Text
24 lines
866 B
Text
#!/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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