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86 lines
3 KiB
Text
86 lines
3 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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include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../modules/ensemblvep/main.nf'
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include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP } 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", "106", [], 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", "106", [], 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", "106", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_vcf_bgzip {
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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_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_vcf_gzip {
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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_GZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], 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", "106", [], 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", "106", [], [], [] )
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}
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