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* update for bcftools merge * Update modules/bcftools/merge/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update modules/bcftools/merge/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated test.yml * added the bed file to the main input tuple * merged all output into one output channel * added a test for bcf.gz output * Update modules/bcftools/merge/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * updated the tests Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
68 lines
3.1 KiB
Text
68 lines
3.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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//keep --no-verson argument, otherwise md5 will change on each execution
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include { BCFTOOLS_MERGE } from '../../../../modules/bcftools/merge/main.nf'
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include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../modules/bcftools/merge/main.nf'
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include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF } from '../../../../modules/bcftools/merge/main.nf'
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workflow test_bcftools_merge {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
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]
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bed = []
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fasta = []
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fasta_fai = []
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BCFTOOLS_MERGE ( input, bed, fasta, fasta_fai )
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}
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workflow test_bcftools_merge_bed {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
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]
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bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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fasta = []
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fasta_fai = []
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BCFTOOLS_MERGE ( input, bed, fasta, fasta_fai )
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}
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workflow test_bcftools_merge_gvcf {
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input = [ [ id:'test' ], // 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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[ file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'], checkIfExists: true) ]
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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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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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BCFTOOLS_MERGE_GVCF ( input, bed, fasta, fasta_fai )
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}
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workflow test_bcftools_merge_bcf {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
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]
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bed = []
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fasta = []
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fasta_fai = []
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BCFTOOLS_MERGE_BCF ( input, bed, fasta, fasta_fai )
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}
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