diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml index 77104e82..c4422150 100644 --- a/subworkflows/nf-core/bam_qc_picard/meta.yml +++ b/subworkflows/nf-core/bam_qc_picard/meta.yml @@ -47,7 +47,7 @@ output: - hs_metrics: type: file description: Alignment metrics files generated by picard CollectHsMetrics - pattern: "*_collecthsmetrics.txt" + pattern: "*_metrics.txt" - wgs_metrics: type: file description: Alignment metrics files generated by picard CollectWgsMetrics diff --git a/tests/subworkflows/nf-core/bam_qc_picard/main.nf b/tests/subworkflows/nf-core/bam_qc_picard/main.nf index 9112416b..03696b44 100644 --- a/tests/subworkflows/nf-core/bam_qc_picard/main.nf +++ b/tests/subworkflows/nf-core/bam_qc_picard/main.nf @@ -6,18 +6,20 @@ include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/m workflow test_bam_qc_picard_wgs { input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - BAM_QC_PICARD ( input, [], [], [] ) + BAM_QC_PICARD ( input, fasta, [], [] ) } workflow test_bam_qc_picard_targetted { input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) bait = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true) - target = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true) + target = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true) - BAM_QC_PICARD ( input, [], bait, target ) + BAM_QC_PICARD ( input, fasta, bait, target ) } diff --git a/tests/subworkflows/nf-core/bam_qc_picard/test.yml b/tests/subworkflows/nf-core/bam_qc_picard/test.yml index af98230d..7b0a6c2b 100644 --- a/tests/subworkflows/nf-core/bam_qc_picard/test.yml +++ b/tests/subworkflows/nf-core/bam_qc_picard/test.yml @@ -30,4 +30,4 @@ - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - - path: ./output/picard/test_collecthsmetrics.txt + - path: ./output/picard/test.CollectHsMetrics.coverage_metrics