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22 lines
817 B
Text
22 lines
817 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_SAMSE } from '../../../../modules/bwa/samse/main.nf' addParams( options: [:] )
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workflow test_bwa_samse {
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Channel
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.fromList(
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[ [ id:'test', single_end:true ],
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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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_SAMSE ( input.join(BWA_ALN.out.sai, by:[0]), BWA_INDEX.out.index )
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}
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