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8d4373b4e8
* added bcftools convert * Update modules/bcftools/convert/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * updated test.yml * Update modules/bcftools/convert/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * added automatic output type detection * linting * removed a trailing whitespace Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
51 lines
1.6 KiB
Text
51 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../modules/bcftools/convert/main.nf'
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include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF } from '../../../../modules/bcftools/convert/main.nf'
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workflow test_bcftools_convert_gvcf {
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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_genome_vcf'], checkIfExists: true),
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[]
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]
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bed = []
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
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}
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workflow test_bcftools_convert_gvcf_bed {
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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_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
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]
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bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
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}
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workflow test_bcftools_convert_gvcf_to_bcf {
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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_genome_vcf'], checkIfExists: true),
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[]
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]
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bed = []
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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BCFTOOLS_CONVERT_BCF ( input, bed, fasta )
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}
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