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Update files and tags for balsamic release 16.0.0 (#117)
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add balsamic release 16.0.0 files
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@mathiasbio
mathiasbio authored Nov 19, 2024
1 parent 378e599 commit 54ae97a
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Showing 8 changed files with 4,053 additions and 2,097 deletions.
359 changes: 189 additions & 170 deletions cg_hermes/config/balsamic.py
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16 changes: 8 additions & 8 deletions cg_hermes/config/balsamic_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,22 +9,22 @@

QC_ALIGNMENT_TAGS = {
# Alignment files (PANEL & WGS)
frozenset(RAW_TAGS["tumor.merged.cram"]): { # cram (tumor)
frozenset(RAW_TAGS["tumor.cram"]): { # cram (tumor)
"tags": ["tumor", "qc-cram"],
"is_mandatory": True,
"used_by": ["deliver"],
},
frozenset(RAW_TAGS["tumor.merged.cram.crai"]): {
frozenset(RAW_TAGS["tumor.cram.crai"]): {
"tags": ["tumor", "qc-cram-index"],
"is_mandatory": True,
"used_by": ["deliver"],
},
frozenset(RAW_TAGS["normal.merged.cram"]): { # cram (normal)
frozenset(RAW_TAGS["normal.cram"]): { # cram (normal)
"tags": ["normal", "qc-cram"],
"is_mandatory": False,
"used_by": ["deliver"],
},
frozenset(RAW_TAGS["normal.merged.cram.crai"]): {
frozenset(RAW_TAGS["normal.cram.crai"]): {
"tags": ["normal", "qc-cram-index"],
"is_mandatory": False,
"used_by": ["deliver"],
Expand All @@ -35,12 +35,12 @@

QC_TUMOR_NORMAL_WGS_TAGS = {
# Alignment files (PANEL & WGS)
frozenset(RAW_TAGS["normal.merged.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.merged.cram.crai"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.cram.crai"]): {"is_mandatory": True},
}

QC_TUMOR_NORMAL_PANEL_TAGS = {
# Alignment files (PANEL & WGS)
frozenset(RAW_TAGS["normal.merged.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.merged.cram.crai"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.cram.crai"]): {"is_mandatory": True},
}
60 changes: 38 additions & 22 deletions cg_hermes/config/balsamic_umi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,22 +8,22 @@

UMI_ALIGNMENT_TAGS = {
# Alignment files
frozenset(RAW_TAGS["tumor_umi_consensusfiltered.merged.cram"]): { # UMI cram (tumor)
frozenset(RAW_TAGS["tumor_umi_consensusfiltered.cram"]): { # UMI cram (tumor)
"tags": ["umi-cram", "tumor"],
"is_mandatory": True,
"used_by": ["deliver", "scout"],
},
frozenset(RAW_TAGS["tumor_umi_consensusfiltered.merged.cram.crai"]): {
frozenset(RAW_TAGS["tumor_umi_consensusfiltered.cram.crai"]): {
"tags": ["umi-cram-index", "tumor"],
"is_mandatory": True,
"used_by": ["deliver", "scout"],
},
frozenset(RAW_TAGS["normal_umi_consensusfiltered.merged.cram"]): { # UMI cram (normal)
frozenset(RAW_TAGS["normal_umi_consensusfiltered.cram"]): { # UMI cram (normal)
"tags": ["umi-cram", "normal"],
"is_mandatory": False,
"used_by": ["deliver", "scout"],
},
frozenset(RAW_TAGS["normal_umi_consensusfiltered.merged.cram.crai"]): {
frozenset(RAW_TAGS["normal_umi_consensusfiltered.cram.crai"]): {
"tags": ["umi-cram-index", "normal"],
"is_mandatory": False,
"used_by": ["deliver", "scout"],
Expand All @@ -42,16 +42,26 @@
"is_mandatory": True,
"used_by": ["deliver"],
},
frozenset(RAW_TAGS["tnscope_umi.research.filtered.pass.vcf.gz"]): {
"tags": ["tnscope-umi", "vcf-umi-snv-research"],
frozenset(RAW_TAGS["tnscope_umi.research.vcf.gz"]): {
"tags": ["tnscope-umi", "vcf-umi-snv-research-unfiltered"],
"is_mandatory": True,
"used_by": ["deliver"],
},
frozenset(RAW_TAGS["tnscope_umi.research.filtered.pass.vcf.gz.tbi"]): {
"tags": ["tnscope-umi", "vcf-umi-snv-research-index"],
frozenset(RAW_TAGS["tnscope_umi.research.vcf.gz.tbi"]): {
"tags": ["tnscope-umi", "vcf-umi-snv-research-unfiltered-index"],
"is_mandatory": True,
"used_by": ["deliver"],
},
frozenset(RAW_TAGS["tnscope_umi.clinical.scored.vcf.gz"]): {
"tags": ["tnscope-umi", "vcf-umi-snv-clinical-scored"],
"is_mandatory": True,
"used_by": ["storage"],
},
frozenset(RAW_TAGS["tnscope_umi.clinical.scored.vcf.gz.tbi"]): {
"tags": ["tnscope-umi", "vcf-umi-snv-clinical-scored-index"],
"is_mandatory": True,
"used_by": ["storage"],
},
frozenset(RAW_TAGS["tnscope_umi.clinical.filtered.pass.vcf.gz"]): {
"tags": ["tnscope-umi", "vcf-umi-snv-clinical"],
"is_mandatory": True,
Expand All @@ -76,25 +86,27 @@
# SNVs/INDELs (PANEL)
frozenset(RAW_TAGS["vardict.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.research.filtered.pass.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.research.filtered.pass.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.clinical.filtered.pass.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.clinical.filtered.pass.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["tnscope.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["tnscope.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.scored.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.scored.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.filtered.pass.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.filtered.pass.vcf.gz.tbi"]): {"is_mandatory": True},
# CNVs (PANEL)
frozenset(RAW_TAGS["tumor.merged.cns"]): {"is_mandatory": True},
frozenset(RAW_TAGS["tumor.merged.cnr"]): {"is_mandatory": True},
frozenset(RAW_TAGS["gene_metrics"]): {"is_mandatory": True},
frozenset(RAW_TAGS["cnvkit.vcf2cytosure.cgh"]): {"is_mandatory": True},
# TMB
frozenset(RAW_TAGS["vardict.balsamic_stat"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.balsamic_stat"]): {"is_mandatory": True},
}

UMI_TUMOR_NORMAL_PANEL_TAGS = {
# Alignment files (PANEL & WGS)
frozenset(RAW_TAGS["normal.merged.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.merged.cram.crai"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal_umi_consensusfiltered.merged.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal_umi_consensusfiltered.merged.cram.crai"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.cram.crai"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal_umi_consensusfiltered.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal_umi_consensusfiltered.cram.crai"]): {"is_mandatory": True},
# Germline SNVs (PANEL & WGS)
frozenset(RAW_TAGS["germline.normal.dnascope.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["germline.normal.dnascope.vcf.gz.tbi"]): {"is_mandatory": True},
Expand All @@ -105,15 +117,19 @@
# SNVs/INDELs (PANEL)
frozenset(RAW_TAGS["vardict.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.research.filtered.pass.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.research.filtered.pass.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.clinical.filtered.pass.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["vardict.clinical.filtered.pass.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["tnscope.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["tnscope.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.scored.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.scored.vcf.gz.tbi"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.filtered.pass.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.clinical.filtered.pass.vcf.gz.tbi"]): {"is_mandatory": True},
# CNVs (PANEL)
frozenset(RAW_TAGS["tumor.merged.cns"]): {"is_mandatory": True},
frozenset(RAW_TAGS["tumor.merged.cnr"]): {"is_mandatory": True},
frozenset(RAW_TAGS["gene_metrics"]): {"is_mandatory": True},
frozenset(RAW_TAGS["cnvkit.vcf2cytosure.cgh"]): {"is_mandatory": True},
# TMB
frozenset(RAW_TAGS["vardict.balsamic_stat"]): {"is_mandatory": True},
frozenset(RAW_TAGS["merged.balsamic_stat"]): {"is_mandatory": True},
# MSI (PANEL UMI)
frozenset(RAW_TAGS["msisensorpro.msi"]): {"is_mandatory": True},
}
14 changes: 14 additions & 0 deletions cg_hermes/constants/tags.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ class VariantTags(StrEnum):
CNV: str = "cnv"
GERMLINE: str = "germline"
MOBILE_ELEMENTS: str = "mobile-elements"
MSI: str = "msi"
NORMAL: str = "normal"
RHOCALL_VIZ: str = "rhocall-viz"
SMN_CALLING: str = "smn-calling"
Expand All @@ -77,6 +78,8 @@ class VariantTags(StrEnum):
VCF_SNV: str = "vcf-snv"
VCF_SNV_CLINICAL: str = "vcf-snv-clinical"
VCF_SNV_CLINICAL_INDEX: str = "vcf-snv-clinical-index"
VCF_SNV_CLINICAL_SCORED: str = "vcf-snv-clinical-scored"
VCF_SNV_CLINICAL_SCORED_INDEX: str = "vcf-snv-clinical-scored-index"
VCF_SNV_FILTERED: str = "vcf-snv-filtered"
VCF_SNV_FILTERED_INDEX: str = "vcf-snv-filtered-index"
VCF_SNV_GERMLINE_NORMAL: str = "vcf-snv-germline-normal"
Expand All @@ -86,6 +89,8 @@ class VariantTags(StrEnum):
VCF_SNV_INDEX: str = "vcf-snv-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"
VCF_SNV_RESEARCH_UNFILTERED_INDEX: str = "vcf-snv-research-unfiltered-index"
VCF_STR: str = "vcf-str"
VCF_STR_INDEX: str = "vcf-str-index"
VCF_SV: str = "vcf-sv"
Expand All @@ -104,6 +109,10 @@ class VariantTags(StrEnum):
VCF_UMI_SNV_INDEX: str = "vcf-umi-snv-index"
VCF_UMI_SNV_RESEARCH: str = "vcf-umi-snv-research"
VCF_UMI_SNV_RESEARCH_INDEX: str = "vcf-umi-snv-research-index"
VCF_UMI_SNV_RESEARCH_UNFILTERED: str = "vcf-umi-snv-research-unfiltered"
VCF_UMI_SNV_RESEARCH_UNFILTERED_INDEX: str = "vcf-umi-snv-research-unfiltered-index"
VCF_UMI_SNV_CLINICAL_RANKED: str = "vcf-umi-snv-clinical-scored"
VCF_UMI_SNV_CLINICAL_RANKED_INDEX: str = "vcf-umi-snv-clinical-scored-index"

@classmethod
def name(cls) -> str:
Expand Down Expand Up @@ -137,6 +146,8 @@ def description(self) -> str:
self.VCF_SNV: "SNV variant call formatted file",
self.VCF_SNV_CLINICAL: "SNV variants from clinical panels",
self.VCF_SNV_CLINICAL_INDEX: "Following index",
self.VCF_SNV_CLINICAL_SCORED: "Scored clinically annotated VCF with SNVs",
self.VCF_SNV_CLINICAL_SCORED_INDEX: "Following index",
self.VCF_SNV_FILTERED: "SNV variants filtered by BALSAMIC",
self.VCF_SNV_FILTERED_INDEX: "Following index",
self.VCF_SNV_GERMLINE_NORMAL: "SNV germline normal variants",
Expand Down Expand Up @@ -164,6 +175,8 @@ def description(self) -> str:
self.VCF_UMI_SNV_INDEX: "Following index",
self.VCF_UMI_SNV_RESEARCH: "SNV UMI variant formatted file",
self.VCF_UMI_SNV_RESEARCH_INDEX: "Following index",
self.VCF_UMI_SNV_CLINICAL_RANKED: "Scored clinically annotated VCF with SNVs from UMI analysis",
self.VCF_UMI_SNV_CLINICAL_RANKED_INDEX: "Following index",
}
return descriptions.get(self, "Description not available")

Expand Down Expand Up @@ -400,6 +413,7 @@ class BioinfoToolsTags(StrEnum):
GFFCOMPARE: str = "gffcompare"
HAPLOTYPE_CALLER: str = "haplotype-caller"
MANTA: str = "manta"
MERGED: str = "merged"
MITODEL: str = "mitodel"
NEXTCLADE: str = "nextclade"
PEDDY: str = "peddy"
Expand Down
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