From 64899fae1ef33247405f4fb42f45418830d9e3c9 Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 21 Aug 2026 10:42:28 +0200 Subject: [PATCH 1/9] Raredisease add concatenated SNV file --- cg_hermes/config/raredisease.py | 10 ++++++++++ cg_hermes/constants/tags.py | 4 ++++ docs/raredisease_map.md | 2 ++ tests/fixtures/raredisease/case_id_deliverables.yaml | 10 ++++++++++ 4 files changed, 26 insertions(+) diff --git a/cg_hermes/config/raredisease.py b/cg_hermes/config/raredisease.py index 3e3fc49..9e57c7d 100644 --- a/cg_hermes/config/raredisease.py +++ b/cg_hermes/config/raredisease.py @@ -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, diff --git a/cg_hermes/constants/tags.py b/cg_hermes/constants/tags.py index 38bb3b6..d4896f5 100644 --- a/cg_hermes/constants/tags.py +++ b/cg_hermes/constants/tags.py @@ -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" @@ -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", diff --git a/docs/raredisease_map.md b/docs/raredisease_map.md index 8569ff9..a3732f4 100644 --- a/docs/raredisease_map.md +++ b/docs/raredisease_map.md @@ -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, 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 | diff --git a/tests/fixtures/raredisease/case_id_deliverables.yaml b/tests/fixtures/raredisease/case_id_deliverables.yaml index 16bc869..ac3a87c 100644 --- a/tests/fixtures/raredisease/case_id_deliverables.yaml +++ b/tests/fixtures/raredisease/case_id_deliverables.yaml @@ -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/CASEID_mt_and_nuclear_snvs.vcf.gz + step: vcf-snv-loqusdb + tag: vcf-snv-loqusdb +- format: vcf + id: CASEID + path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi + step: vcf-snv-loqusdb + tag: vcf-snv-loqusdb_index - format: vcf id: CASEID path: PATHTOCASE/call_snv/mitochondria/CASEID_mitochondria.vcf.gz From f53bc657c5b4be2f1bf925f13a58a7634ebd37be Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 21 Aug 2026 10:47:53 +0200 Subject: [PATCH 2/9] fix naming convention --- cg_hermes/config/raredisease.py | 4 ++-- docs/raredisease_map.md | 4 ++-- tests/fixtures/raredisease/case_id_deliverables.yaml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cg_hermes/config/raredisease.py b/cg_hermes/config/raredisease.py index 9e57c7d..2815f6e 100644 --- a/cg_hermes/config/raredisease.py +++ b/cg_hermes/config/raredisease.py @@ -171,12 +171,12 @@ "is_mandatory": False, "used_by": [UsageTags.CG], }, - frozenset(["call_snv_loqusdb", "call_snv_loqusdb"]): { + frozenset(["call_snv", "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"]): { + frozenset(["call_snv", "call_snv_loqusdb_index"]): { "tags": [VariantTags.VCF_SNV_LOQUSDB_INDEX], "is_mandatory": False, "used_by": [UsageTags.CG, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE], diff --git a/docs/raredisease_map.md b/docs/raredisease_map.md index a3732f4..5d54b6d 100644 --- a/docs/raredisease_map.md +++ b/docs/raredisease_map.md @@ -28,8 +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, call_snv_loqusdb_index | True | vcf-snv-loqusdb-index | cg, clinical-delivery, long-term-storage | +| call_snv | True | vcf-snv-loqusdb | cg, clinical-delivery, long-term-storage | +| call_snv, 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 | diff --git a/tests/fixtures/raredisease/case_id_deliverables.yaml b/tests/fixtures/raredisease/case_id_deliverables.yaml index ac3a87c..829f1c6 100644 --- a/tests/fixtures/raredisease/case_id_deliverables.yaml +++ b/tests/fixtures/raredisease/case_id_deliverables.yaml @@ -263,12 +263,12 @@ files: - format: vcf id: CASEID path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz - step: vcf-snv-loqusdb + step: call_snv tag: vcf-snv-loqusdb - format: vcf id: CASEID path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi - step: vcf-snv-loqusdb + step: call_snv tag: vcf-snv-loqusdb_index - format: vcf id: CASEID From 093f055e15a7fc6c2f7ca5ace206b318ec573189 Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 21 Aug 2026 10:54:36 +0200 Subject: [PATCH 3/9] typo --- docs/raredisease_map.md | 2 +- tests/fixtures/raredisease/case_id_deliverables.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/raredisease_map.md b/docs/raredisease_map.md index 5d54b6d..24cd77e 100644 --- a/docs/raredisease_map.md +++ b/docs/raredisease_map.md @@ -28,7 +28,7 @@ | 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 | True | vcf-snv-loqusdb | cg, clinical-delivery, long-term-storage | +| call_snv, call_snv_loqusdb | True | vcf-snv-loqusdb | cg, clinical-delivery, long-term-storage | | call_snv, 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 | diff --git a/tests/fixtures/raredisease/case_id_deliverables.yaml b/tests/fixtures/raredisease/case_id_deliverables.yaml index 829f1c6..67acb86 100644 --- a/tests/fixtures/raredisease/case_id_deliverables.yaml +++ b/tests/fixtures/raredisease/case_id_deliverables.yaml @@ -264,12 +264,12 @@ files: id: CASEID path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz step: call_snv - tag: vcf-snv-loqusdb + tag: call_snv-loqusdb - format: vcf id: CASEID path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi step: call_snv - tag: vcf-snv-loqusdb_index + tag: call_snv-loqusdb_index - format: vcf id: CASEID path: PATHTOCASE/call_snv/mitochondria/CASEID_mitochondria.vcf.gz From d2519340f7115fca4fbad83899018075fcd9e135 Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 21 Aug 2026 11:02:17 +0200 Subject: [PATCH 4/9] hyphen --- tests/fixtures/raredisease/case_id_deliverables.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/fixtures/raredisease/case_id_deliverables.yaml b/tests/fixtures/raredisease/case_id_deliverables.yaml index 67acb86..d4d3d7d 100644 --- a/tests/fixtures/raredisease/case_id_deliverables.yaml +++ b/tests/fixtures/raredisease/case_id_deliverables.yaml @@ -264,12 +264,12 @@ files: id: CASEID path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz step: call_snv - tag: call_snv-loqusdb + tag: call_snv_loqusdb - format: vcf id: CASEID path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi step: call_snv - tag: call_snv-loqusdb_index + tag: call_snv_loqusdb_index - format: vcf id: CASEID path: PATHTOCASE/call_snv/mitochondria/CASEID_mitochondria.vcf.gz From 3b1a75f80189d09fdc15379efbe5b723097abdde Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 31 Aug 2026 09:16:55 +0200 Subject: [PATCH 5/9] update fixture file paths --- tests/fixtures/raredisease/case_id_deliverables.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/fixtures/raredisease/case_id_deliverables.yaml b/tests/fixtures/raredisease/case_id_deliverables.yaml index d4d3d7d..dd7417e 100644 --- a/tests/fixtures/raredisease/case_id_deliverables.yaml +++ b/tests/fixtures/raredisease/case_id_deliverables.yaml @@ -262,12 +262,12 @@ files: tag: call_snv_index - format: vcf id: CASEID - path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz + path: PATHTOCASE/call_snv/concatenated_calls/CASEID_mt_and_nuclear_snvs.vcf.gz step: call_snv tag: call_snv_loqusdb - format: vcf id: CASEID - path: PATHTOCASE/call_snv/concatenated/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi + path: PATHTOCASE/call_snv/concatenated_calls/CASEID_mt_and_nuclear_snvs.vcf.gz.tbi step: call_snv tag: call_snv_loqusdb_index - format: vcf From e8ab5735c642ea4c81726228d35ba205750c18a9 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 31 Aug 2026 09:37:50 +0200 Subject: [PATCH 6/9] tag name --- tests/fixtures/raredisease/case_id_deliverables.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/fixtures/raredisease/case_id_deliverables.yaml b/tests/fixtures/raredisease/case_id_deliverables.yaml index dd7417e..8837feb 100644 --- a/tests/fixtures/raredisease/case_id_deliverables.yaml +++ b/tests/fixtures/raredisease/case_id_deliverables.yaml @@ -263,12 +263,12 @@ files: - format: vcf id: CASEID path: PATHTOCASE/call_snv/concatenated_calls/CASEID_mt_and_nuclear_snvs.vcf.gz - step: call_snv + 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 + step: call_snv_loqusdb tag: call_snv_loqusdb_index - format: vcf id: CASEID From 7da483086f1aee2f2899bf34b43e92579921fab0 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 31 Aug 2026 09:39:36 +0200 Subject: [PATCH 7/9] also change in config --- cg_hermes/config/raredisease.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cg_hermes/config/raredisease.py b/cg_hermes/config/raredisease.py index 2815f6e..9e57c7d 100644 --- a/cg_hermes/config/raredisease.py +++ b/cg_hermes/config/raredisease.py @@ -171,12 +171,12 @@ "is_mandatory": False, "used_by": [UsageTags.CG], }, - frozenset(["call_snv", "call_snv_loqusdb"]): { + 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", "call_snv_loqusdb_index"]): { + 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], From d2097803aa0126b11b424880050ab4b5cbc764f5 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 31 Aug 2026 09:44:01 +0200 Subject: [PATCH 8/9] same as in servers --- cg_hermes/config/raredisease.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cg_hermes/config/raredisease.py b/cg_hermes/config/raredisease.py index 9e57c7d..2815f6e 100644 --- a/cg_hermes/config/raredisease.py +++ b/cg_hermes/config/raredisease.py @@ -171,12 +171,12 @@ "is_mandatory": False, "used_by": [UsageTags.CG], }, - frozenset(["call_snv_loqusdb", "call_snv_loqusdb"]): { + frozenset(["call_snv", "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"]): { + frozenset(["call_snv", "call_snv_loqusdb_index"]): { "tags": [VariantTags.VCF_SNV_LOQUSDB_INDEX], "is_mandatory": False, "used_by": [UsageTags.CG, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE], From 1330df1c978908b27d9350041cddffbe437e9f53 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 31 Aug 2026 10:34:32 +0200 Subject: [PATCH 9/9] change step name --- cg_hermes/config/raredisease.py | 4 ++-- docs/raredisease_map.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cg_hermes/config/raredisease.py b/cg_hermes/config/raredisease.py index 2815f6e..9e57c7d 100644 --- a/cg_hermes/config/raredisease.py +++ b/cg_hermes/config/raredisease.py @@ -171,12 +171,12 @@ "is_mandatory": False, "used_by": [UsageTags.CG], }, - frozenset(["call_snv", "call_snv_loqusdb"]): { + 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", "call_snv_loqusdb_index"]): { + 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], diff --git a/docs/raredisease_map.md b/docs/raredisease_map.md index 24cd77e..473d1cb 100644 --- a/docs/raredisease_map.md +++ b/docs/raredisease_map.md @@ -28,8 +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, call_snv_loqusdb | True | vcf-snv-loqusdb | cg, clinical-delivery, long-term-storage | -| call_snv, call_snv_loqusdb_index | True | vcf-snv-loqusdb-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 |