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25 lines
970 B
Text
25 lines
970 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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consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
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gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
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fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
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def use_fasta = true
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def use_gtf = true
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QUAST( consensus, fasta, gff, use_fasta, use_gtf )
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}
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workflow test_quast_noref {
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consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
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gff = file('gff_dummy')
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fasta = file('fasta_dummy')
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def use_fasta = false
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def use_gtf = false
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QUAST( consensus, fasta, use_fasta, gff, use_gtf)
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}
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