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c9256616b9
* update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
25 lines
862 B
Text
25 lines
862 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { QUAST } from '../../../software/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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