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a25423dbb9
* add gatk4/combinegvcfs module * update gatk4/combinegvcfs * loop to create a string adding -V to each vcf file * add contains for variable md5 * rm whitespace * meta in output * fix indentations * fix indentations * move tmpdir to args and update conda version Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
24 lines
1.1 KiB
Text
24 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_COMBINEGVCFS } from '../../../../modules/gatk4/combinegvcfs/main.nf'
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workflow test_gatk4_combinegvcfs {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_idx'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_COMBINEGVCFS ( input, fasta, fasta_fai, fasta_dict )
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}
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