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Adjust nallo deliverable requirements for NBS #171

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Adjust nallo deliverable requirements for NBS #171

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4eb1ce7
make methylation peddy and repeats optional
Jul 29, 2026
0cb6fee
Merge branch 'main' into nbs-nallo
ieduba Jul 29, 2026
050da0f
make phasing optional
Jul 29, 2026
ad063d1
Merge branch 'nbs-nallo' of github.com:Clinical-Genomics/hermes into …
Jul 29, 2026
6df667d
make most sv callers optional
Jul 29, 2026
92db1fd
whatshap optional
Jul 29, 2026
662bd58
hificnv depth optional
Jul 29, 2026
41f19d1
pedigree optional
Jul 31, 2026
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66 changes: 33 additions & 33 deletions cg_hermes/config/nallo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,12 +23,12 @@
NALLO_COMMON_TAGS = {
frozenset(["alignment", "alignment_haplotags"]): {
"tags": [AlignmentTags.BAM, NalloTags.HAPLOTAGS],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["alignment", "alignment_haplotags_index"]): {
"tags": [AlignmentTags.BAM_INDEX, NalloTags.HAPLOTAGS],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["assembly", "summary_hap1"]): {
Expand Down Expand Up @@ -93,37 +93,37 @@
},
frozenset(["methylation_pileup", "methbat_hap1"]): {
"tags": [AnalysisTags.BED, NalloTags.HAP1, BioinfoToolsTags.METHBAT_PILEUP],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["methylation_pileup", "methbat_hap1_index"]): {
"tags": [AnalysisTags.BED_INDEX, NalloTags.HAP1, BioinfoToolsTags.METHBAT_PILEUP],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["methylation_pileup", "methbat_hap2"]): {
"tags": [AnalysisTags.BED, NalloTags.HAP2, BioinfoToolsTags.METHBAT_PILEUP],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["methylation_pileup", "methbat_hap2_index"]): {
"tags": [AnalysisTags.BED_INDEX, NalloTags.HAP2, BioinfoToolsTags.METHBAT_PILEUP],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["methylation_pileup", "methbat_combined"]): {
"tags": [AnalysisTags.BED, NalloTags.COMBINED, BioinfoToolsTags.METHBAT_PILEUP],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["methylation_pileup", "methbat_combined_index"]): {
"tags": [AnalysisTags.BED_INDEX, NalloTags.COMBINED, BioinfoToolsTags.METHBAT_PILEUP],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["methylation_calling", "methbat_profile"]): {
"tags": [NalloTags.METHYLATION_TSV, BioinfoToolsTags.METHBAT_PROFILE],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset({"multiqc", "multiqc-html"}): {
Expand All @@ -133,7 +133,7 @@
},
frozenset(["pedigree", "pedigree_fam"]): {
"tags": [FamilyTags.PEDIGREE],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.SCOUT, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["sambamba_depth", "qc_bam"]): {
Expand Down Expand Up @@ -163,17 +163,17 @@
},
frozenset(["peddy", "peddy"]): {
"tags": [BioinfoToolsTags.PEDDY, FamilyTags.PED],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.AUDIT, UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY],
},
frozenset(["peddy", "ped_check"]): {
"tags": [BioinfoToolsTags.PEDDY, QCTags.PED_CHECK],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.AUDIT, UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY],
},
frozenset(["peddy", "sex_check"]): {
"tags": [BioinfoToolsTags.PEDDY, QCTags.SEX_CHECK],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.AUDIT, UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY],
},
frozenset(["deepvariant", "report"]): {
Expand All @@ -183,17 +183,17 @@
},
frozenset(["paraphase", "paraphase"]): {
"tags": [AlignmentTags.BAM, BioinfoToolsTags.PARAPHASE],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["paraphase", "paraphase_index"]): {
"tags": [AlignmentTags.BAM_INDEX, BioinfoToolsTags.PARAPHASE],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["paraphase", "json"]): {
"tags": [BioinfoToolsTags.PARAPHASE, ReportTags.JSON],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["paraphrase", "json"]): {
Expand All @@ -218,32 +218,32 @@
},
frozenset(["sorted_repeats", "vcf_str"]): {
"tags": [NalloTags.REPEATS, NalloTags.SORTED, VariantTags.VCF],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["sorted_repeats", "vcf_str_index"]): {
"tags": [NalloTags.REPEATS, NalloTags.SORTED, VariantTags.VCF_INDEX],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["spanning_repeats", "bam"]): {
"tags": [NalloTags.REPEATS, NalloTags.SPANNING, AlignmentTags.BAM],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["spanning_repeats", "bam_index"]): {
"tags": [NalloTags.REPEATS, NalloTags.SPANNING, AlignmentTags.BAM_INDEX],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["repeats_annotated", "vcf_str"]): {
"tags": [VariantTags.VCF_STR],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["repeats_annotated", "vcf_str_index"]): {
"tags": [VariantTags.VCF_STR_INDEX],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["trgt", "variant_catalog"]): {
Expand Down Expand Up @@ -293,32 +293,32 @@
},
frozenset(["svs_per_caller", "vcf_hificnv"]): {
"tags": [BioinfoToolsTags.HIFICNV, VariantTags.VCF],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["svs_per_caller", "vcf_hificnv_index"]): {
"tags": [BioinfoToolsTags.HIFICNV, VariantTags.VCF_INDEX],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["svs_per_caller", "vcf_sawfish"]): {
"tags": [BioinfoToolsTags.SAWFISH, VariantTags.VCF],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["svs_per_caller", "vcf_sawfish_index"]): {
"tags": [BioinfoToolsTags.SAWFISH, VariantTags.VCF_INDEX],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["svs_per_caller", "vcf_severus"]): {
"tags": [BioinfoToolsTags.SEVERUS, VariantTags.VCF],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["svs_per_caller", "vcf_severus_index"]): {
"tags": [BioinfoToolsTags.SEVERUS, VariantTags.VCF_INDEX],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.LONG_TERM_STORAGE],
},
frozenset(["svs_per_caller", "vcf_sniffles"]): {
Expand All @@ -338,17 +338,17 @@
},
frozenset(["copy_number", "bedgraph"]): {
"tags": [VariantTags.CNV, NalloTags.BEDGRAPH],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["depth_track", "bigwig"]): {
"tags": [BioinfoToolsTags.HIFICNV, AnalysisTags.BIGWIG],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["maf_depth_track", "bigwig"]): {
"tags": [BioinfoToolsTags.HIFICNV, AnalysisTags.BIGWIG, NalloTags.MAF],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["gens_generatedata", "baf"]): {
Expand All @@ -373,12 +373,12 @@
},
frozenset(["phase_blocks", "gtf"]): {
"tags": [BioinfoToolsTags.WHATSHAP, AnalysisTags.PHASE_BLOCKS],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset(["phase_blocks", "gtf_index"]): {
"tags": [BioinfoToolsTags.WHATSHAP, AnalysisTags.PHASE_BLOCKS_INDEX],
"is_mandatory": True,
"is_mandatory": False,
"used_by": [UsageTags.SCOUT, UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
},
frozenset({"multiqc", "multiqc-json"}): {
Expand Down
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