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34 lines
1.2 KiB
Text
34 lines
1.2 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf'
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include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../modules/biscuit/align/main.nf'
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include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../modules/biscuit/align/main.nf'
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// Single-end test
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workflow test_biscuit_align_single {
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input = [ [ id:'test' ], // 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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BISCUIT_INDEX ( fasta )
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BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
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}
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// paired-end test
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workflow test_biscuit_align_paired {
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input = [ [ id:'test' ], // 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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BISCUIT_INDEX ( fasta )
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BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
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}
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