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e0d820f9f4
* feat: add snpeff * fix: linting * fix: tests * fix: add csv output * fix: add params information * fix: improve script * Update software/snpeff/environment.yml * Update software/snpeff/environment.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * fix test Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
12 lines
386 B
Text
12 lines
386 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SNPEFF } from '../../../software/snpeff/main.nf' addParams( snpeff_tag: '5.0.WBcel235', use_cache: false )
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workflow test_snpeff {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
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]
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SNPEFF ( input, "WBcel235.99", [] )
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}
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