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28 lines
1 KiB
Text
28 lines
1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
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include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
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workflow test_diamond_blastx {
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db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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out_ext = 'tfdfdt' // Nonsense file extension to check default case.
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blast_columns = 'qseqid qlen'
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DIAMOND_MAKEDB ( db )
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DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
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}
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workflow test_diamond_blastx_daa {
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db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
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fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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out_ext = 'daa'
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blast_columns = []
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DIAMOND_MAKEDB ( db )
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DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
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}
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