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25 lines
954 B
Text
25 lines
954 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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Channel
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.fromList(
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[
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[ id:'test', single_end:false ],
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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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).collect()
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.set { input }
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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 ( input.join(BWA_ALN.out.sai), BWA_INDEX.out.index )
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}
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