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24 lines
913 B
Text
24 lines
913 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SOMALIER_EXTRACT } from '../../../../modules/somalier/extract/main.nf'
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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sites = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/sites_chr21.hg38.vcf.gz", checkIfExists: true)
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workflow test_somalier_extract {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true)
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]
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SOMALIER_EXTRACT ( input, [fasta, fasta_fai], sites )
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}
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