diff --git a/modules/delly/call/main.nf b/modules/delly/call/main.nf index 2cfbcffd..19a47c96 100644 --- a/modules/delly/call/main.nf +++ b/modules/delly/call/main.nf @@ -8,8 +8,7 @@ process DELLY_CALL { 'quay.io/biocontainers/delly:1.1.3--h358d541_0' }" input: - tuple val(meta), path(input), path(input_index) - path exclude_bed + tuple val(meta), path(input), path(input_index), path(exclude_bed) path fasta path fai diff --git a/tests/modules/delly/call/main.nf b/tests/modules/delly/call/main.nf index 29d2d3f8..78dc7c37 100644 --- a/tests/modules/delly/call/main.nf +++ b/tests/modules/delly/call/main.nf @@ -8,37 +8,37 @@ workflow test_delly_call_bam { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + [] ] - exclude_regions = [] 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) - DELLY_CALL ( input, exclude_regions, fasta, fai ) + DELLY_CALL ( input, fasta, fai ) } workflow test_delly_call_cram { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [] ] - exclude_regions = [] 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) - DELLY_CALL ( input, exclude_regions, fasta, fai ) + DELLY_CALL ( input, fasta, fai ) } workflow test_delly_call_exclude_regions { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) ] - exclude_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], 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) - DELLY_CALL ( input, exclude_regions, fasta, fai ) + DELLY_CALL ( input, fasta, fai ) }