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Update Nallo to 0.11.0 #159

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10 changes: 10 additions & 0 deletions cg_hermes/config/nallo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,6 +200,16 @@
"is_mandatory": True,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["paraphrase", "json"]): {
"tags": [BioinfoToolsTags.PARAPHRASE, ReportTags.JSON],
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["paraphrase", "tsv"]): {
"tags": [BioinfoToolsTags.PARAPHRASE, ReportTags.TSV],
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["paraphase", "vcf"]): {
"tags": [BioinfoToolsTags.PARAPHASE, VariantTags.VCF],
"is_mandatory": False,
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2 changes: 2 additions & 0 deletions cg_hermes/constants/tags.py
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Expand Up @@ -429,6 +429,7 @@ class BioinfoToolsTags(StrEnum):
MODKIT_PILEUP: str = "modkit-pileup"
NEXTCLADE: str = "nextclade"
PARAPHASE: str = "paraphase"
PARAPHRASE: str = "paraphrase"
PEDDY: str = "peddy"
PICARD: str = "picard"
PIZZLY: str = "pizzly"
Expand Down Expand Up @@ -489,6 +490,7 @@ def description(self) -> str:
self.MODKIT_PILEUP: "Modkit pileup tool output",
self.NEXTCLADE: "Viral genome clade assignment",
self.PARAPHASE: "Paraphase tool output",
self.PARAPHRASE: "Paraphrase annotated paraphase JSONs",
self.PEDDY: "Tool to check pedigree and ancestral relations",
self.PICARD: "Picard set of bioinformatic tools",
self.PIZZLY: "Fusion caller",
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2 changes: 2 additions & 0 deletions docs/nallo_map.md
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Expand Up @@ -36,6 +36,8 @@
| paraphase | True | bam, paraphase | clinical-delivery, long-term-storage |
| paraphase_index, paraphase | True | bam-index, paraphase | clinical-delivery, long-term-storage |
| json, paraphase | True | paraphase, json | clinical-delivery, long-term-storage |
| json, paraphrase | False | paraphrase, json | clinical-delivery, long-term-storage |
| tsv, paraphrase | False | paraphrase, tsv | clinical-delivery, long-term-storage |
| vcf, paraphase | False | paraphase, vcf | clinical-delivery, long-term-storage |
| vcf_index, paraphase | False | paraphase, vcf-index | clinical-delivery, long-term-storage |
| sambamba_depth | True | coverage, sambamba_depth | cg, long-term-storage |
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14 changes: 12 additions & 2 deletions tests/fixtures/nallo/case_id_deliverables.yaml
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Expand Up @@ -426,10 +426,20 @@ files:
step: paraphase
tag: paraphase_index
- format: json
id: CASEID
path: PATHTOCASE/paraphase/family/CASEID/CASEID_merged.json
id: SAMPLEID
path: PATHTOCASE/paraphase/sample/SAMPLEID/SAMPLEID.paraphase.json
step: paraphase
tag: json
- format: json
id: CASEID
path: PATHTOCASE/paraphase/family/CASEID/CASEID_annotated.json
step: paraphrase
tag: json
- format: tsv
id: CASEID
path: PATHTOCASE/paraphase/family/CASEID/CASEID_annotated.tsv
step: paraphrase
tag: tsv
- format: vcf
id: CASEID
path: PATHTOCASE/paraphase/family/CASEID/CASEID_paraphase_merged.vcf.gz
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