From f6a5b9d9c7b7a8b073975acf43342fe680182bb3 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Thu, 2 May 2024 16:35:52 +0200 Subject: [PATCH 1/4] Update use_read_count_threshold for taxprofiler --- cg/meta/workflow/nf_analysis.py | 2 +- cg/meta/workflow/raredisease.py | 6 ++++++ cg/meta/workflow/rnafusion.py | 6 ++++++ cg/meta/workflow/taxprofiler.py | 6 ++++++ cg/meta/workflow/tomte.py | 6 ++++++ 5 files changed, 25 insertions(+), 1 deletion(-) diff --git a/cg/meta/workflow/nf_analysis.py b/cg/meta/workflow/nf_analysis.py index b8022ff302..4effed7380 100644 --- a/cg/meta/workflow/nf_analysis.py +++ b/cg/meta/workflow/nf_analysis.py @@ -89,7 +89,7 @@ def process(self, process: Process): def use_read_count_threshold(self) -> bool: """Defines whether the threshold for adequate read count should be passed for all samples when determining if the analysis for a case should be automatically started.""" - return True + return NotImplementedError @property def sample_sheet_headers(self) -> list[str]: diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py index 3b038f5655..657b5854be 100644 --- a/cg/meta/workflow/raredisease.py +++ b/cg/meta/workflow/raredisease.py @@ -113,3 +113,9 @@ def get_managed_variants(self) -> list[str]: def get_workflow_metrics(self) -> dict: return RAREDISEASE_METRIC_CONDITIONS + + @property + def use_read_count_threshold(self) -> bool: + """Defines whether the threshold for adequate read count should be passed for all samples + when determining if the analysis for a case should be automatically started.""" + return True \ No newline at end of file diff --git a/cg/meta/workflow/rnafusion.py b/cg/meta/workflow/rnafusion.py index 20d06bc91c..7284b41a2a 100644 --- a/cg/meta/workflow/rnafusion.py +++ b/cg/meta/workflow/rnafusion.py @@ -122,3 +122,9 @@ def ensure_mandatory_metrics_present(metrics: list[MetricsBase]) -> None: def get_workflow_metrics(self) -> dict: return RNAFUSION_METRIC_CONDITIONS + + @property + def use_read_count_threshold(self) -> bool: + """Defines whether the threshold for adequate read count should be passed for all samples + when determining if the analysis for a case should be automatically started.""" + return True \ No newline at end of file diff --git a/cg/meta/workflow/taxprofiler.py b/cg/meta/workflow/taxprofiler.py index 9d5f985018..ddb8d89c94 100644 --- a/cg/meta/workflow/taxprofiler.py +++ b/cg/meta/workflow/taxprofiler.py @@ -104,3 +104,9 @@ def get_multiqc_search_patterns(self, case_id: str) -> dict: def get_genome_build(self, case_id: str) -> str: """Return the reference genome build version of a Taxprofiler analysis.""" return GenomeVersion.T2T_CHM13.value + + @property + def use_read_count_threshold(self) -> bool: + """Defines whether the threshold for adequate read count should be passed for all samples + when determining if the analysis for a case should be automatically started.""" + return False \ No newline at end of file diff --git a/cg/meta/workflow/tomte.py b/cg/meta/workflow/tomte.py index 11fed68209..d1a3fab522 100644 --- a/cg/meta/workflow/tomte.py +++ b/cg/meta/workflow/tomte.py @@ -82,3 +82,9 @@ def get_workflow_parameters(self, case_id: str) -> TomteParameters: def get_workflow_metrics(self) -> dict: return TOMTE_METRIC_CONDITIONS + + @property + def use_read_count_threshold(self) -> bool: + """Defines whether the threshold for adequate read count should be passed for all samples + when determining if the analysis for a case should be automatically started.""" + return True \ No newline at end of file From 55b9e8da646cf3803dcf9347fbf300e5df752e0b Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Thu, 2 May 2024 16:47:44 +0200 Subject: [PATCH 2/4] Black --- cg/meta/workflow/raredisease.py | 2 +- cg/meta/workflow/rnafusion.py | 2 +- cg/meta/workflow/taxprofiler.py | 2 +- cg/meta/workflow/tomte.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py index 657b5854be..aaede4d66a 100644 --- a/cg/meta/workflow/raredisease.py +++ b/cg/meta/workflow/raredisease.py @@ -118,4 +118,4 @@ def get_workflow_metrics(self) -> dict: def use_read_count_threshold(self) -> bool: """Defines whether the threshold for adequate read count should be passed for all samples when determining if the analysis for a case should be automatically started.""" - return True \ No newline at end of file + return True diff --git a/cg/meta/workflow/rnafusion.py b/cg/meta/workflow/rnafusion.py index 7284b41a2a..a7b78e7f96 100644 --- a/cg/meta/workflow/rnafusion.py +++ b/cg/meta/workflow/rnafusion.py @@ -127,4 +127,4 @@ def get_workflow_metrics(self) -> dict: def use_read_count_threshold(self) -> bool: """Defines whether the threshold for adequate read count should be passed for all samples when determining if the analysis for a case should be automatically started.""" - return True \ No newline at end of file + return True diff --git a/cg/meta/workflow/taxprofiler.py b/cg/meta/workflow/taxprofiler.py index ddb8d89c94..85408a8efc 100644 --- a/cg/meta/workflow/taxprofiler.py +++ b/cg/meta/workflow/taxprofiler.py @@ -109,4 +109,4 @@ def get_genome_build(self, case_id: str) -> str: def use_read_count_threshold(self) -> bool: """Defines whether the threshold for adequate read count should be passed for all samples when determining if the analysis for a case should be automatically started.""" - return False \ No newline at end of file + return False diff --git a/cg/meta/workflow/tomte.py b/cg/meta/workflow/tomte.py index d1a3fab522..de78f92ffe 100644 --- a/cg/meta/workflow/tomte.py +++ b/cg/meta/workflow/tomte.py @@ -87,4 +87,4 @@ def get_workflow_metrics(self) -> dict: def use_read_count_threshold(self) -> bool: """Defines whether the threshold for adequate read count should be passed for all samples when determining if the analysis for a case should be automatically started.""" - return True \ No newline at end of file + return True From a8fd21b8c59f3147d006628c16c81accd7b868b7 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Thu, 2 May 2024 16:54:32 +0200 Subject: [PATCH 3/4] Update --- cg/meta/workflow/nf_analysis.py | 2 +- cg/meta/workflow/raredisease.py | 5 ----- cg/meta/workflow/rnafusion.py | 6 ------ cg/meta/workflow/tomte.py | 6 ------ 4 files changed, 1 insertion(+), 18 deletions(-) diff --git a/cg/meta/workflow/nf_analysis.py b/cg/meta/workflow/nf_analysis.py index 4effed7380..b8022ff302 100644 --- a/cg/meta/workflow/nf_analysis.py +++ b/cg/meta/workflow/nf_analysis.py @@ -89,7 +89,7 @@ def process(self, process: Process): def use_read_count_threshold(self) -> bool: """Defines whether the threshold for adequate read count should be passed for all samples when determining if the analysis for a case should be automatically started.""" - return NotImplementedError + return True @property def sample_sheet_headers(self) -> list[str]: diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py index aaede4d66a..534594695c 100644 --- a/cg/meta/workflow/raredisease.py +++ b/cg/meta/workflow/raredisease.py @@ -114,8 +114,3 @@ def get_managed_variants(self) -> list[str]: def get_workflow_metrics(self) -> dict: return RAREDISEASE_METRIC_CONDITIONS - @property - def use_read_count_threshold(self) -> bool: - """Defines whether the threshold for adequate read count should be passed for all samples - when determining if the analysis for a case should be automatically started.""" - return True diff --git a/cg/meta/workflow/rnafusion.py b/cg/meta/workflow/rnafusion.py index a7b78e7f96..20d06bc91c 100644 --- a/cg/meta/workflow/rnafusion.py +++ b/cg/meta/workflow/rnafusion.py @@ -122,9 +122,3 @@ def ensure_mandatory_metrics_present(metrics: list[MetricsBase]) -> None: def get_workflow_metrics(self) -> dict: return RNAFUSION_METRIC_CONDITIONS - - @property - def use_read_count_threshold(self) -> bool: - """Defines whether the threshold for adequate read count should be passed for all samples - when determining if the analysis for a case should be automatically started.""" - return True diff --git a/cg/meta/workflow/tomte.py b/cg/meta/workflow/tomte.py index de78f92ffe..11fed68209 100644 --- a/cg/meta/workflow/tomte.py +++ b/cg/meta/workflow/tomte.py @@ -82,9 +82,3 @@ def get_workflow_parameters(self, case_id: str) -> TomteParameters: def get_workflow_metrics(self) -> dict: return TOMTE_METRIC_CONDITIONS - - @property - def use_read_count_threshold(self) -> bool: - """Defines whether the threshold for adequate read count should be passed for all samples - when determining if the analysis for a case should be automatically started.""" - return True From f714c1bc35f01c45ee68a20ee49b178f3c25851d Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Thu, 2 May 2024 16:55:33 +0200 Subject: [PATCH 4/4] Remove extra space --- cg/meta/workflow/raredisease.py | 1 - 1 file changed, 1 deletion(-) diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py index 534594695c..3b038f5655 100644 --- a/cg/meta/workflow/raredisease.py +++ b/cg/meta/workflow/raredisease.py @@ -113,4 +113,3 @@ def get_managed_variants(self) -> list[str]: def get_workflow_metrics(self) -> dict: return RAREDISEASE_METRIC_CONDITIONS -