diff --git a/tests/modules/gatk4/markduplicatesspark/main.nf b/tests/modules/gatk4/markduplicatesspark/main.nf index 2f294f59..cd02c240 100644 --- a/tests/modules/gatk4/markduplicatesspark/main.nf +++ b/tests/modules/gatk4/markduplicatesspark/main.nf @@ -6,18 +6,32 @@ include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markdupli workflow test_gatk4_markduplicates_spark { input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict ) } +// chr 22 workflow test_gatk4_markduplicates_spark_multiple_bams { input = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + ] ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict ) +} + +// chr 21 +workflow test_gatk4_markduplicates_spark_multiple_bams_21 { + input = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) ] ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)