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update tests
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3 changed files with 9 additions and 7 deletions
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@ -47,7 +47,7 @@ output:
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- hs_metrics:
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- hs_metrics:
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type: file
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type: file
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description: Alignment metrics files generated by picard CollectHsMetrics
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description: Alignment metrics files generated by picard CollectHsMetrics
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pattern: "*_collecthsmetrics.txt"
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pattern: "*_metrics.txt"
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- wgs_metrics:
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- wgs_metrics:
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type: file
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type: file
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description: Alignment metrics files generated by picard CollectWgsMetrics
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description: Alignment metrics files generated by picard CollectWgsMetrics
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@ -6,18 +6,20 @@ include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/m
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workflow test_bam_qc_picard_wgs {
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workflow test_bam_qc_picard_wgs {
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input = [ [ id:'test', single_end:false ], // meta map
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BAM_QC_PICARD ( input, [], [], [] )
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BAM_QC_PICARD ( input, fasta, [], [] )
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}
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}
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workflow test_bam_qc_picard_targetted {
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workflow test_bam_qc_picard_targetted {
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input = [ [ id:'test', single_end:false ], // meta map
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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bait = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
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bait = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
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target = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
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target = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
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BAM_QC_PICARD ( input, [], bait, target )
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BAM_QC_PICARD ( input, fasta, bait, target )
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}
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}
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@ -30,4 +30,4 @@
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- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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- path: ./output/picard/test_collecthsmetrics.txt
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- path: ./output/picard/test.CollectHsMetrics.coverage_metrics
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