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14 lines
666 B
Text
14 lines
666 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FGBIO_SORTBAM } from '../../../../software/fgbio/sortbam/main.nf' addParams( options: [args: '-s TemplateCoordinate', suffix: '_out'] )
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include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../software/fgbio/callmolecularconsensusreads/main.nf' addParams( options: [args: '-M 1', suffix: '_molreads'] )
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workflow test_fgbio_callmolecularconsensusreads {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
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FGBIO_SORTBAM ( input )
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FGBIO_CALLMOLECULARCONSENSUSREADS ( FGBIO_SORTBAM.out.bam )
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}
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