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update tests

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This commit is contained in:
Matthias De Smet 2022-04-28 10:19:30 +02:00
parent 3cbf5c63e5
commit 881e9db4bf
3 changed files with 9 additions and 7 deletions
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2
subworkflows/nf-core/bam_qc_picard/meta.yml
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@ -47,7 +47,7 @@ output:
- hs_metrics: - hs_metrics:
type: file type: file
description: Alignment metrics files generated by picard CollectHsMetrics description: Alignment metrics files generated by picard CollectHsMetrics
pattern: "*_collecthsmetrics.txt" pattern: "*_metrics.txt"
- wgs_metrics: - wgs_metrics:
type: file type: file
description: Alignment metrics files generated by picard CollectWgsMetrics description: Alignment metrics files generated by picard CollectWgsMetrics

12
tests/subworkflows/nf-core/bam_qc_picard/main.nf
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@ -6,18 +6,20 @@ include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/m
workflow test_bam_qc_picard_wgs { workflow test_bam_qc_picard_wgs {
input = [ [ id:'test', single_end:false ], // meta map 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 { workflow test_bam_qc_picard_targetted {
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_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) 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 )
} }

2
tests/subworkflows/nf-core/bam_qc_picard/test.yml
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@ -30,4 +30,4 @@
- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics - 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_by_cycle_metrics
- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- path: ./output/picard/test_collecthsmetrics.txt - path: ./output/picard/test.CollectHsMetrics.coverage_metrics