From 5fe256a4bd3cbf45fa5f8333e7a3cfa68dcfad73 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 13:47:02 -0500 Subject: [PATCH 1/9] Update snps_and_indels.py --- runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py | 1 + 1 file changed, 1 insertion(+) diff --git a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py index fa8fe4dd4..49b50e460 100755 --- a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py +++ b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py @@ -665,6 +665,7 @@ def get_request_id_runs(self, app): .order_by("-created_date") .first() .operator_run.runs.all() + .filter(status=RunStatus.COMPLETED) ) if not len(most_recent_runs_for_request): raise Exception("No matching Nucleo runs found for request {}".format(self.request_id)) From 13073b429c40a3f733b92eff3e5a327e02797fcd Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 13:47:41 -0500 Subject: [PATCH 2/9] Update snps_and_indels.py --- .../operator/access/v2_1_0/snps_and_indels/snps_and_indels.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py index 49b50e460..b81fae08a 100755 --- a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py +++ b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py @@ -651,10 +651,6 @@ def get_request_id_runs(self, app): :param request_id: str - IGO request ID :return: List[str] - List of most recent runs from given request ID """ - # if not request_id: - # request_id_runs = Run.objects.filter(pk__in=self.run_ids) - # self.request_id = most_recent_runs_for_request[0].tags["igoRequestId"] - # else: most_recent_runs_for_request = ( Run.objects.filter( tags__igoRequestId=self.request_id, From 9a909f46a296b33c97f2adf7b5b6955008da1907 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 15:27:05 -0500 Subject: [PATCH 3/9] Update access_nucleo_qc.py --- runner/operator/access/v2_1_0/qc/access_nucleo_qc.py | 1 + 1 file changed, 1 insertion(+) diff --git a/runner/operator/access/v2_1_0/qc/access_nucleo_qc.py b/runner/operator/access/v2_1_0/qc/access_nucleo_qc.py index 170251982..2cf810b5a 100644 --- a/runner/operator/access/v2_1_0/qc/access_nucleo_qc.py +++ b/runner/operator/access/v2_1_0/qc/access_nucleo_qc.py @@ -89,6 +89,7 @@ def get_nucleo_outputs(self): .order_by("-created_date") .first() .operator_run.runs.all() + .filter(status=RunStatus.COMPLETED) ) if not len(most_recent_runs_for_request): raise Exception("No matching Access V2 Nucleo runs found for request {}".format(self.request_id)) From 65dc39542032ce3c75182734d95f75085a417d75 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 17:24:01 -0500 Subject: [PATCH 4/9] matched normal edge case --- .../access/v2_1_0/snps_and_indels/snps_and_indels.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py index b81fae08a..0f28fdc51 100755 --- a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py +++ b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py @@ -703,10 +703,12 @@ def construct_sample_inputs(self, sample_info): .replace("-simplex.bam", "-CURATED-SIMPLEX") ] - matched_normal = [_create_cwl_bam_object(sample_info["matched_normal_unfiltered"][0].path)] - matched_normal_id = [ - sample_info["matched_normal_unfiltered"][0].file_name.replace(UNCOLLAPSED_BAM_STEM, "") - ] + if sample_info["matched_normal_unfiltered"][0] == None: + matched_normal = [] + matched_normal_id = [''] + else: + matched_normal = [_create_cwl_bam_object(sample_info["matched_normal_unfiltered"][0].path)] + matched_normal_id = [sample_info["matched_normal_unfiltered"][0].file_name.replace(UNCOLLAPSED_BAM_STEM, "")] genotyping_bams = ( normal_bam_duplex + normal_bam_simplex + tumor_bam_duplex + tumor_bam_simplex + matched_normal From 7dacaa7db4a43debf3d3b1458fa62d6ccd016fc5 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 17:24:13 -0500 Subject: [PATCH 5/9] Update snps_and_indels.py --- .../access/v2_1_0/snps_and_indels/snps_and_indels.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py index 0f28fdc51..38ddc521e 100755 --- a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py +++ b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py @@ -705,10 +705,12 @@ def construct_sample_inputs(self, sample_info): if sample_info["matched_normal_unfiltered"][0] == None: matched_normal = [] - matched_normal_id = [''] + matched_normal_id = [""] else: - matched_normal = [_create_cwl_bam_object(sample_info["matched_normal_unfiltered"][0].path)] - matched_normal_id = [sample_info["matched_normal_unfiltered"][0].file_name.replace(UNCOLLAPSED_BAM_STEM, "")] + matched_normal = [_create_cwl_bam_object(sample_info["matched_normal_unfiltered"][0].path)] + matched_normal_id = [ + sample_info["matched_normal_unfiltered"][0].file_name.replace(UNCOLLAPSED_BAM_STEM, "") + ] genotyping_bams = ( normal_bam_duplex + normal_bam_simplex + tumor_bam_duplex + tumor_bam_simplex + matched_normal From 8e4b9109fdce89e3a632c55c4817366c3f038ce5 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 17:42:35 -0500 Subject: [PATCH 6/9] Update snps_and_indels.py --- .../v2_1_0/snps_and_indels/snps_and_indels.py | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py index 38ddc521e..adc225b17 100755 --- a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py +++ b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py @@ -703,21 +703,25 @@ def construct_sample_inputs(self, sample_info): .replace("-simplex.bam", "-CURATED-SIMPLEX") ] + + genotyping_bams_ids = ( + tumor_duplex_id + tumor_simplex_id + normal_duplex_id + normal_simplex_id + ) + + genotyping_bams = ( + normal_bam_duplex + normal_bam_simplex + tumor_bam_duplex + tumor_bam_simplex + ) + if sample_info["matched_normal_unfiltered"][0] == None: - matched_normal = [] matched_normal_id = [""] else: matched_normal = [_create_cwl_bam_object(sample_info["matched_normal_unfiltered"][0].path)] matched_normal_id = [ sample_info["matched_normal_unfiltered"][0].file_name.replace(UNCOLLAPSED_BAM_STEM, "") ] - - genotyping_bams = ( - normal_bam_duplex + normal_bam_simplex + tumor_bam_duplex + tumor_bam_simplex + matched_normal - ) - genotyping_bams_ids = ( - tumor_duplex_id + tumor_simplex_id + normal_duplex_id + normal_simplex_id + matched_normal_id - ) + genotyping_bams_ids += matched_normal_id + matched_normal_id += matched_normal + for key, files in sample_info.items(): for f in files: From 5cd674f8abbf4adbdd2fecb03a0a66e3924102a5 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 17:47:27 -0500 Subject: [PATCH 7/9] Update snps_and_indels.py --- .../access/v2_1_0/snps_and_indels/snps_and_indels.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py index adc225b17..d4ca28710 100755 --- a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py +++ b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py @@ -703,14 +703,9 @@ def construct_sample_inputs(self, sample_info): .replace("-simplex.bam", "-CURATED-SIMPLEX") ] + genotyping_bams_ids = tumor_duplex_id + tumor_simplex_id + normal_duplex_id + normal_simplex_id - genotyping_bams_ids = ( - tumor_duplex_id + tumor_simplex_id + normal_duplex_id + normal_simplex_id - ) - - genotyping_bams = ( - normal_bam_duplex + normal_bam_simplex + tumor_bam_duplex + tumor_bam_simplex - ) + genotyping_bams = normal_bam_duplex + normal_bam_simplex + tumor_bam_duplex + tumor_bam_simplex if sample_info["matched_normal_unfiltered"][0] == None: matched_normal_id = [""] @@ -721,7 +716,6 @@ def construct_sample_inputs(self, sample_info): ] genotyping_bams_ids += matched_normal_id matched_normal_id += matched_normal - for key, files in sample_info.items(): for f in files: From 4a3cc8c47fb24a567c4f55efcc7b506efccb780c Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 3 Feb 2025 17:48:53 -0500 Subject: [PATCH 8/9] Update snps_and_indels.py --- .../operator/access/v2_1_0/snps_and_indels/snps_and_indels.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py index d4ca28710..e6fcc7943 100755 --- a/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py +++ b/runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py @@ -715,7 +715,7 @@ def construct_sample_inputs(self, sample_info): sample_info["matched_normal_unfiltered"][0].file_name.replace(UNCOLLAPSED_BAM_STEM, "") ] genotyping_bams_ids += matched_normal_id - matched_normal_id += matched_normal + genotyping_bams += matched_normal for key, files in sample_info.items(): for f in files: From d219e05b7496a8d915713647c7fc5154fedcee6a Mon Sep 17 00:00:00 2001 From: Sinisa Ivkovic Date: Tue, 4 Feb 2025 13:45:48 -0500 Subject: [PATCH 9/9] Version bump 1.91.4 --- beagle/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beagle/__init__.py b/beagle/__init__.py index cd044473b..baf754747 100644 --- a/beagle/__init__.py +++ b/beagle/__init__.py @@ -1 +1 @@ -__version__ = "1.91.3" +__version__ = "1.91.4"