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Raredisease add concatenated SNV file for loqusDB #172

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Merged
peterpru merged 9 commits into from
Sep 1, 2026
Merged

Raredisease add concatenated SNV file for loqusDB #172

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64899fa
Raredisease add concatenated SNV file
peterpru Aug 21, 2026
f53bc65
fix naming convention
peterpru Aug 21, 2026
093f055
typo
peterpru Aug 21, 2026
d251934
hyphen
peterpru Aug 21, 2026
3b1a75f
update fixture file paths
peterpru Aug 31, 2026
e8ab573
tag name
peterpru Aug 31, 2026
7da4830
also change in config
peterpru Aug 31, 2026
d209780
same as in servers
peterpru Aug 31, 2026
1330df1
change step name
peterpru Aug 31, 2026
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10 changes: 10 additions & 0 deletions cg_hermes/config/raredisease.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,6 +171,16 @@
"is_mandatory": False,
"used_by": [UsageTags.CG],
},
frozenset(["call_snv_loqusdb", "call_snv_loqusdb"]): {
"tags": [VariantTags.VCF_SNV_LOQUSDB],
"is_mandatory": True,
"used_by": [UsageTags.CG, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["call_snv_loqusdb", "call_snv_loqusdb_index"]): {
"tags": [VariantTags.VCF_SNV_LOQUSDB_INDEX],
"is_mandatory": False,
"used_by": [UsageTags.CG, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["call_sv", "call_sv"]): {
"tags": [VariantTags.VCF_SV],
"is_mandatory": False,
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4 changes: 4 additions & 0 deletions cg_hermes/constants/tags.py
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Expand Up @@ -87,6 +87,8 @@ class VariantTags(StrEnum):
VCF_SNV_GERMLINE_TUMOR: str = "vcf-snv-germline-tumor"
VCF_SNV_GERMLINE_TUMOR_INDEX: str = "vcf-snv-germline-tumor-index"
VCF_SNV_INDEX: str = "vcf-snv-index"
VCF_SNV_LOQUSDB: str = "vcf-snv-loqusdb"
VCF_SNV_LOQUSDB_INDEX: str = "vcf-snv-loqusdb-index"
VCF_SNV_RESEARCH: str = "vcf-snv-research"
VCF_SNV_RESEARCH_INDEX: str = "vcf-snv-research-index"
VCF_SNV_RESEARCH_UNFILTERED: str = "vcf-snv-research-unfiltered"
Expand Down Expand Up @@ -155,6 +157,8 @@ def description(self) -> str:
self.VCF_SNV_GERMLINE_TUMOR: "SNV germline tumor variants",
self.VCF_SNV_GERMLINE_TUMOR_INDEX: "Following index",
self.VCF_SNV_INDEX: "Following index",
self.VCF_SNV_LOQUSDB: "Concatenated MT and SNV variants",
self.VCF_SNV_LOQUSDB_INDEX: "Following index",
self.VCF_SNV_RESEARCH: "SNV variants from whole genome",
self.VCF_SNV_RESEARCH_INDEX: "Following index",
self.VCF_STR: "Short tandem repeat variants",
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2 changes: 2 additions & 0 deletions docs/raredisease_map.md
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Expand Up @@ -28,6 +28,8 @@
| research_index, annotate_mobile_elements | False | mobile-elements, research, vcf-index | scout, clinical-delivery, long-term-storage |
| call_snv | True | vcf-snv | genotype, clinical-delivery, long-term-storage |
| call_snv_index, call_snv | False | vcf-snv-index | cg, clinical-delivery, long-term-storage |
| call_snv_loqusdb | True | vcf-snv-loqusdb | cg, clinical-delivery, long-term-storage |
| call_snv_loqusdb_index | True | vcf-snv-loqusdb-index | cg, clinical-delivery, long-term-storage |
| call_snv_mt, call_snv | False | vcf-snv, mitochondria | cg |
| call_snv, call_snv_mt_index | False | vcf-snv-index, mitochondria | cg |
| call_sv | False | vcf-sv | cg, clinical-delivery, long-term-storage |
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10 changes: 10 additions & 0 deletions tests/fixtures/raredisease/case_id_deliverables.yaml
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Expand Up @@ -260,6 +260,16 @@ files:
path: PATHTOCASE/call_snv/genome/CASEID_snv.vcf.gz.tbi
step: call_snv
tag: call_snv_index
- format: vcf
id: CASEID
path: PATHTOCASE/call_snv/concatenated_calls/CASEID_mt_and_nuclear_snvs.vcf.gz
step: call_snv_loqusdb
tag: call_snv_loqusdb
- format: vcf
id: CASEID
path: PATHTOCASE/call_snv/concatenated_calls/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi
step: call_snv_loqusdb
tag: call_snv_loqusdb_index
- format: vcf
id: CASEID
path: PATHTOCASE/call_snv/mitochondria/CASEID_mitochondria.vcf.gz
Expand Down
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