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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
25 lines
861 B
Text
25 lines
861 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { QUAST } from '../../../modules/quast/main.nf' addParams(options: [:])
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workflow test_quast_ref {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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gff = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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consensus = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
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use_fasta = true
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use_gtf = true
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QUAST ( consensus, fasta, gff, use_fasta, use_gtf )
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}
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workflow test_quast_noref {
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fasta = file('fasta_dummy')
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gff = file('gff_dummy')
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consensus = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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use_fasta = false
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use_gtf = false
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QUAST ( consensus, fasta, gff, use_fasta, use_gtf )
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}
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