From 0f1e54fdaeef8903f6f428b38fa6e395249773ff Mon Sep 17 00:00:00 2001 From: jemten Date: Thu, 5 Oct 2023 15:28:59 +0200 Subject: [PATCH] fixing tests --- 643594-miptest_metrics_deliverables.yaml | 3 +++ definitions/rd_dna_panel_parameters.yaml | 2 +- definitions/rd_dna_parameters.yaml | 2 +- definitions/rd_rna_parameters.yaml | 2 +- ...etric_-v1.3-.yaml => qc_eval_metric_-v1.4-.yaml} | 2 ++ t/define_evaluate_metric.t | 13 ++++++++++--- t/evaluate_analysis.t | 2 +- 7 files changed, 19 insertions(+), 7 deletions(-) create mode 100644 643594-miptest_metrics_deliverables.yaml rename t/data/references/{qc_eval_metric_-v1.3-.yaml => qc_eval_metric_-v1.4-.yaml} (96%) diff --git a/643594-miptest_metrics_deliverables.yaml b/643594-miptest_metrics_deliverables.yaml new file mode 100644 index 000000000..0381bacc5 --- /dev/null +++ b/643594-miptest_metrics_deliverables.yaml @@ -0,0 +1,3 @@ +--- +metrics: [] + diff --git a/definitions/rd_dna_panel_parameters.yaml b/definitions/rd_dna_panel_parameters.yaml index e7ad57c26..a6a68718e 100755 --- a/definitions/rd_dna_panel_parameters.yaml +++ b/definitions/rd_dna_panel_parameters.yaml @@ -1183,7 +1183,7 @@ qccollect_eval_metric_file: associated_recipe: - qccollect_ar data_type: SCALAR - default: qc_eval_metric_-v1.3-.yaml + default: qc_eval_metric_-v1.4-.yaml exists_check: file is_reference: 1 reference: reference_dir diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml index 3b8b2e8f0..ec546e7a2 100755 --- a/definitions/rd_dna_parameters.yaml +++ b/definitions/rd_dna_parameters.yaml @@ -2309,7 +2309,7 @@ qccollect_eval_metric_file: associated_recipe: - qccollect_ar data_type: SCALAR - default: qc_eval_metric_-v1.3-.yaml + default: qc_eval_metric_-v1.4-.yaml exists_check: file is_reference: 1 reference: reference_dir diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml index 508b6578c..61239b52d 100755 --- a/definitions/rd_rna_parameters.yaml +++ b/definitions/rd_rna_parameters.yaml @@ -1095,7 +1095,7 @@ qccollect_eval_metric_file: associated_recipe: - qccollect_ar data_type: SCALAR - default: qc_eval_metric_-v1.3-.yaml + default: qc_eval_metric_-v1.4-.yaml exists_check: file is_reference: 1 reference: reference_dir diff --git a/t/data/references/qc_eval_metric_-v1.3-.yaml b/t/data/references/qc_eval_metric_-v1.4-.yaml similarity index 96% rename from t/data/references/qc_eval_metric_-v1.3-.yaml rename to t/data/references/qc_eval_metric_-v1.4-.yaml index 656479d98..61f935624 100644 --- a/t/data/references/qc_eval_metric_-v1.3-.yaml +++ b/t/data/references/qc_eval_metric_-v1.4-.yaml @@ -28,6 +28,8 @@ wgs: collectmultiplemetrics: PCT_PF_READS_ALIGNED: lt: 0.95 + PCT_PF_READS_IMPROPER_PAIRS: + gt: 0.05 PCT_ADAPTER: gt: 0.0005 markduplicates: diff --git a/t/define_evaluate_metric.t b/t/define_evaluate_metric.t index df02b66e2..e753ac6f0 100644 --- a/t/define_evaluate_metric.t +++ b/t/define_evaluate_metric.t @@ -47,8 +47,9 @@ diag( q{Test define_evaluate_metric from Qccollect.pm} . $SPACE . $EXECUTABLE_NAME ); -Readonly my $PCT_ADAPTER => 0.0005; -Readonly my $PCT_PF_READS_ALIGNED => 0.95; +Readonly my $PCT_ADAPTER => 0.0005; +Readonly my $PCT_PF_READS_ALIGNED => 0.95; +Readonly my $PCT_PF_READS_IMPROPER_PAIRS => 0.05; my $log = test_log( { no_screen => 1, } ); @@ -59,7 +60,7 @@ my %sample_info = test_mip_hashes( ); ## Given a file with evaluation metrics -my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.3-.yaml} ); +my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.4-.yaml} ); ## When defining the evaluation metrics based on the analysis my %evaluate_metric = define_evaluate_metric( @@ -83,6 +84,9 @@ my %expected = ( PCT_PF_READS_ALIGNED => { lt => $PCT_PF_READS_ALIGNED, }, + PCT_PF_READS_IMPROPER_PAIRS => { + gt => $PCT_PF_READS_IMPROPER_PAIRS, + }, }, }, ADM1059A2 => { @@ -98,6 +102,9 @@ my %expected = ( PCT_PF_READS_ALIGNED => { lt => $PCT_PF_READS_ALIGNED, }, + PCT_PF_READS_IMPROPER_PAIRS => { + gt => $PCT_PF_READS_IMPROPER_PAIRS, + }, }, }, ADM1059A3 => { diff --git a/t/evaluate_analysis.t b/t/evaluate_analysis.t index d8b16e958..8ab27e0aa 100644 --- a/t/evaluate_analysis.t +++ b/t/evaluate_analysis.t @@ -69,7 +69,7 @@ my %sample_info = test_mip_hashes( } ); -my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.3-.yaml} ); +my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.4-.yaml} ); ## Then set the relevant evaluation metrics for the analysis my $is_ok = evaluate_analysis(