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18 lines
645 B
Text
18 lines
645 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GRAPHMAP2_INDEX } from '../../../../software/graphmap2/index/main.nf' addParams( options: [:] )
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include { GRAPHMAP2_ALIGN } from '../../../../software/graphmap2/align/main.nf' addParams( options: [:] )
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workflow test_graphmap2_align {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['nanopore']['test_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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GRAPHMAP2_INDEX ( fasta )
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GRAPHMAP2_ALIGN ( input, fasta, GRAPHMAP2_INDEX.out.index )
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}
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