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30f72e2482
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774 * Trying to fix tests * Still trying to fix tests * Fetching the vep-output-file-extension from the args. * Update meta.yml * WIP: Adding tests for vep-output json and tab * updated the test.yml Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
62 lines
2.1 KiB
Text
62 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
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include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../modules/ensemblvep/main.nf'
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include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../modules/ensemblvep/main.nf'
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include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../modules/ensemblvep/main.nf'
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workflow test_ensemblvep_fasta_json {
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input = [
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[ 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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_tab {
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input = [
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[ 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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_vcf {
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input = [
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[ 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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta {
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input = [
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[ 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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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}
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workflow test_ensemblvep_no_fasta {
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input = [
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[ 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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ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [], [] )
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}
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