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https://github.com/MillironX/nf-core_modules.git
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4f1c1601cf
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * Add sampe * Fix container paths * Update based on code review from @grst * Update input docs
20 lines
854 B
Text
20 lines
854 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
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include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
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include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' addParams( options: [:] )
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workflow test_bwa_sampe {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], 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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BWA_INDEX ( fasta )
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BWA_ALN ( input, BWA_INDEX.out.index )
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BWA_SAMPE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
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}
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