nf-core_modules/tests/software/snpeff/main.nf
Maxime U. Garcia e0d820f9f4
Add snpeff (#546)
* 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>
2021-07-06 13:40:55 +01:00

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Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SNPEFF } from '../../../software/snpeff/main.nf' addParams( snpeff_tag: '5.0.WBcel235', use_cache: false )
workflow test_snpeff {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
]
SNPEFF ( input, "WBcel235.99", [] )
}