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43 lines
2.3 KiB
Text
43 lines
2.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
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include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
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workflow test_gatk4_markduplicates_spark {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], 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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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
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}
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// chr 22
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workflow test_gatk4_markduplicates_spark_multiple_bams {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], 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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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
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}
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// chr 22
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workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], 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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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MARKDUPLICATES_SPARK_METRICS ( input, fasta, fai, dict )
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}
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