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33 lines
1.2 KiB
Text
33 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
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include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf' addParams( options: [:] )
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//
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// Test with single-end data
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//
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workflow test_bwameth_align_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_methylated_1_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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BWAMETH_INDEX ( fasta )
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BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
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}
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//
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// Test with paired-end data
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//
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workflow test_bwameth_align_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_methylated_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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BWAMETH_INDEX ( fasta )
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BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
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}
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