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fixed tests - mixed chr21 + chr22

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SusiJo 2022-05-25 16:38:30 +02:00
parent dd6d838cd7
commit 1400f2e683
1 changed files with 19 additions and 5 deletions
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24
tests/modules/gatk4/markduplicatesspark/main.nf
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@ -6,18 +6,32 @@ include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markdupli
workflow test_gatk4_markduplicates_spark { workflow test_gatk4_markduplicates_spark {
input = [ [ id:'test', single_end:false ], // meta map 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) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict ) GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
} }
// chr 22
workflow test_gatk4_markduplicates_spark_multiple_bams { workflow test_gatk4_markduplicates_spark_multiple_bams {
input = [ [ id:'test', single_end:false ], // meta map 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) 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) fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)