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23 lines
962 B
Text
23 lines
962 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/bbmap/bbsplit/main.nf' addParams( options: [:] )
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include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/bbmap/bbsplit/main.nf' addParams( options: [:] )
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workflow test_bbmap_bbsplit {
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input = [
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[ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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bbsplit_fasta_list = [
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['human'],
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file('https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/chr22_23800000-23980000.fa', checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BBMAP_BBSPLIT_INDEX ( [ [:], [] ], [], fasta, bbsplit_fasta_list, true )
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BBMAP_BBSPLIT_SPLIT ( input, BBMAP_BBSPLIT_INDEX.out.index, fasta, bbsplit_fasta_list, true )
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}
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