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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
15 lines
527 B
Text
15 lines
527 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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params.save_mpileup = true
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include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf' addParams( [ options: [args2: '-aa -A -d 0 -Q 0'] ] )
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workflow test_ivar_consensus {
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input = [ [ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], 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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IVAR_CONSENSUS ( input, fasta )
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}
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