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Feature/nucleo snv #1412

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merged 10 commits into from
Feb 4, 2025
Merged

Feature/nucleo snv #1412

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5fe256a
Update snps_and_indels.py
Feb 3, 2025
13073b4
Update snps_and_indels.py
Feb 3, 2025
9a909f4
Update access_nucleo_qc.py
Feb 3, 2025
65dc395
matched normal edge case
Feb 3, 2025
7dacaa7
Update snps_and_indels.py
Feb 3, 2025
8e4b910
Update snps_and_indels.py
Feb 3, 2025
5cd674f
Update snps_and_indels.py
Feb 3, 2025
4a3cc8c
Update snps_and_indels.py
Feb 3, 2025
df4114b
Merge branch 'feature/nucleo_snv' of github.com:mskcc/beagle into fea…
sivkovic Feb 4, 2025
d219e05
Version bump 1.91.4
sivkovic Feb 4, 2025
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2 changes: 1 addition & 1 deletion beagle/__init__.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "1.91.3"
__version__ = "1.91.4"
1 change: 1 addition & 0 deletions runner/operator/access/v2_1_0/qc/access_nucleo_qc.py
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Expand Up @@ -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))
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27 changes: 13 additions & 14 deletions runner/operator/access/v2_1_0/snps_and_indels/snps_and_indels.py
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Expand Up @@ -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,
Expand All @@ -665,6 +661,7 @@ 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))
Expand Down Expand Up @@ -706,17 +703,19 @@ 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, "")
]
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 + matched_normal
)
genotyping_bams_ids = (
tumor_duplex_id + tumor_simplex_id + normal_duplex_id + normal_simplex_id + matched_normal_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_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_ids += matched_normal_id
genotyping_bams += matched_normal

for key, files in sample_info.items():
for f in files:
Expand Down