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adjusted input to use queryname sorted bams

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SusiJo 2022-05-31 14:35:18 +02:00
parent 39e34418c9
commit e0e8273f74
1 changed files with 11 additions and 10 deletions
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21
tests/modules/gatk4/markduplicatesspark/main.nf
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@ -3,6 +3,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf' include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
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
@ -18,8 +19,8 @@ workflow test_gatk4_markduplicates_spark {
// chr 22 // 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_name_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_name_sorted_bam'], checkIfExists: true)
] ] ] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -28,15 +29,15 @@ workflow test_gatk4_markduplicates_spark_multiple_bams {
GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict ) GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
} }
// chr 21 // chr 22
workflow test_gatk4_markduplicates_spark_multiple_bams_21 { workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
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_name_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_name_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_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict ) GATK4_MARKDUPLICATES_SPARK_METRICS ( input, fasta, fai, dict )
} }