From 4eb1ce773243a4068ca2ee94cc2c823a11409eee Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Jul 2026 08:07:26 +0200 Subject: [PATCH 1/6] make methylation peddy and repeats optional --- cg_hermes/config/nallo.py | 38 +++++++++++++++++++------------------- docs/nallo_map.md | 34 +++++++++++++++++----------------- 2 files changed, 36 insertions(+), 36 deletions(-) diff --git a/cg_hermes/config/nallo.py b/cg_hermes/config/nallo.py index d78730e..7fcc620 100644 --- a/cg_hermes/config/nallo.py +++ b/cg_hermes/config/nallo.py @@ -92,37 +92,37 @@ }, 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(["qc_bam", "mosdepth_d4"]): { @@ -167,17 +167,17 @@ }, 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"]): { @@ -187,17 +187,17 @@ }, 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(["paraphase", "vcf"]): { @@ -212,32 +212,32 @@ }, 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"]): { diff --git a/docs/nallo_map.md b/docs/nallo_map.md index 089501c..70818bb 100644 --- a/docs/nallo_map.md +++ b/docs/nallo_map.md @@ -16,22 +16,22 @@ | modkit_hap2_index, methylation_pileup | False | bed-index, hap2, modkit-pileup | clinical-delivery, long-term-storage | | modkit_ungrouped, methylation_pileup | False | bed, ungrouped, modkit-pileup | clinical-delivery, long-term-storage | | modkit_ungrouped_index, methylation_pileup | False | bed-index, ungrouped, modkit-pileup | clinical-delivery, long-term-storage | -| methbat_hap1, methylation_pileup | True | bed, hap1, methbat-pileup | clinical-delivery, long-term-storage | -| methbat_hap1_index, methylation_pileup | True | bed-index, hap1, methbat-pileup | clinical-delivery, long-term-storage | -| methbat_hap2, methylation_pileup | True | bed, hap2, methbat-pileup | clinical-delivery, long-term-storage | -| methbat_hap2_index, methylation_pileup | True | bed-index, hap2, methbat-pileup | clinical-delivery, long-term-storage | -| methbat_combined, methylation_pileup | True | bed, combined, methbat-pileup | clinical-delivery, long-term-storage | -| methbat_combined_index, methylation_pileup | True | bed-index, combined, modkit-pileup | clinical-delivery, long-term-storage | -| methbat_profile, methylation_calling | True | methylation-tsv, methbat-profile | scout, clinical-delivery, long-term-storage | -| mosdepth_d4, qc_bam | False | coverage, d4 | scout, clinical-delivery, long-term-storage | +| methbat_hap1, methylation_pileup | False | bed, hap1, methbat-pileup | clinical-delivery, long-term-storage | +| methbat_hap1_index, methylation_pileup | False | bed-index, hap1, methbat-pileup | clinical-delivery, long-term-storage | +| methbat_hap2, methylation_pileup | False | bed, hap2, methbat-pileup | clinical-delivery, long-term-storage | +| methbat_hap2_index, methylation_pileup | False | bed-index, hap2, methbat-pileup | clinical-delivery, long-term-storage | +| methbat_combined, methylation_pileup | False | bed, combined, methbat-pileup | clinical-delivery, long-term-storage | +| methbat_combined_index, methylation_pileup | False | bed-index, combined, modkit-pileup | clinical-delivery, long-term-storage | +| methbat_profile, methylation_calling | False | methylation-tsv, methbat-profile | scout, clinical-delivery, long-term-storage | +| mosdepth_d4, qc_bam | False | coverage, d4 | scout, clinical-delivery, long-term-storage | | multiqc-html, multiqc | True | multiqc-html | scout, clinical-delivery, long-term-storage | | pedigree_fam, pedigree | True | pedigree | clinical-delivery, scout, long-term-storage | | relate_html, somalier | True | somalier, relate-html | clinical-delivery, scout, long-term-storage | | relate_pairs, somalier | True | somalier, relate-pairs | scout, long-term-storage | | relate_samples, somalier | True | somalier, relate-samples | scout, long-term-storage | -| peddy | True | peddy, ped | audit, scout, clinical-delivery | -| ped_check, peddy | True | peddy, ped-check | audit, scout, clinical-delivery | -| peddy, sex_check | True | peddy, sex-check | audit, scout, clinical-delivery | +| peddy | False | peddy, ped | audit, scout, clinical-delivery | +| ped_check, peddy | False | peddy, ped-check | audit, scout, clinical-delivery | +| peddy, sex_check | False | peddy, sex-check | audit, scout, clinical-delivery | | deepvariant, report | True | deepvariant-report | clinical-delivery, long-term-storage | | paraphase | True | bam, paraphase | clinical-delivery, long-term-storage | | paraphase_index, paraphase | True | bam-index, paraphase | clinical-delivery, long-term-storage | @@ -39,12 +39,12 @@ | 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 | -| sorted_repeats, vcf_str | True | repeats, sorted, vcf | long-term-storage | -| sorted_repeats, vcf_str_index | True | repeats, sorted, vcf-index | long-term-storage | -| spanning_repeats, bam | True | repeats, spanning, bam | long-term-storage | -| spanning_repeats, bam_index | True | repeats, spanning, bam-index | long-term-storage | -| repeats_annotated, vcf_str | True | vcf-str | scout, clinical-delivery, long-term-storage | -| repeats_annotated, vcf_str_index | True | vcf-str-index | scout, clinical-delivery, long-term-storage | +| sorted_repeats, vcf_str | False | repeats, sorted, vcf | long-term-storage | +| sorted_repeats, vcf_str_index | False | repeats, sorted, vcf-index | long-term-storage | +| spanning_repeats, bam | False | repeats, spanning, bam | long-term-storage | +| spanning_repeats, bam_index | False | repeats, spanning, bam-index | long-term-storage | +| repeats_annotated, vcf_str | False | vcf-str | scout, clinical-delivery, long-term-storage | +| repeats_annotated, vcf_str_index | False | vcf-str-index | scout, clinical-delivery, long-term-storage | | trgt, variant_catalog | True | trgt, variant-catalog | scout, long-term-storage | | vcf_snv_research, snv_annotated | True | vcf-snv-research | scout, clinical-delivery, long-term-storage | | vcf_snv_research_index, snv_annotated | True | vcf-snv-research-index | scout, clinical-delivery, long-term-storage | From 050da0fbac7a5c910fc49dc9d9bf4b8cc2f28e95 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Jul 2026 08:52:40 +0200 Subject: [PATCH 2/6] make phasing optional --- cg_hermes/config/nallo.py | 4 ++-- docs/nallo_map.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cg_hermes/config/nallo.py b/cg_hermes/config/nallo.py index 7fcc620..1401e8e 100644 --- a/cg_hermes/config/nallo.py +++ b/cg_hermes/config/nallo.py @@ -22,12 +22,12 @@ 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"]): { diff --git a/docs/nallo_map.md b/docs/nallo_map.md index 70818bb..603ae21 100644 --- a/docs/nallo_map.md +++ b/docs/nallo_map.md @@ -1,7 +1,7 @@ | Nallo tags | Mandatory | HK tags | Used by | |-----------------------------------------------------|-------------|-------------------------------------|---------------------------------------------| -| alignment_haplotags, alignment | True | bam, haplotags | scout, clinical-delivery, long-term-storage | -| alignment_haplotags_index, alignment | True | bam-index, haplotags | scout, clinical-delivery, long-term-storage | +| alignment_haplotags, alignment | False | bam, haplotags | scout, clinical-delivery, long-term-storage | +| alignment_haplotags_index, alignment | False | bam-index, haplotags | scout, clinical-delivery, long-term-storage | | assembly, summary_hap1 | False | hap1, assembly, assembly-summary | clinical-delivery, long-term-storage | | summary_hap2, assembly | False | hap2, assembly, assembly-summary | clinical-delivery, long-term-storage | | assembly_aligned, assembly | False | bam, assembly | clinical-delivery, long-term-storage | From 6df667dab3ad2fd4ef184675bb9e873cecbde2b4 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Jul 2026 09:25:18 +0200 Subject: [PATCH 3/6] make most sv callers optional --- cg_hermes/config/nallo.py | 12 ++++++------ docs/nallo_map.md | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/cg_hermes/config/nallo.py b/cg_hermes/config/nallo.py index 85f915a..dc53bd6 100644 --- a/cg_hermes/config/nallo.py +++ b/cg_hermes/config/nallo.py @@ -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"]): { diff --git a/docs/nallo_map.md b/docs/nallo_map.md index 85e7134..91a16f3 100644 --- a/docs/nallo_map.md +++ b/docs/nallo_map.md @@ -54,12 +54,12 @@ | vcf_sv_research_index, sv_annotated_ranked | True | vcf-sv-research-index | scout, clinical-delivery, long-term-storage | | vcf_sv_clinical, sv_annotated_ranked_filtered | True | vcf-sv-clinical | scout, clinical-delivery, long-term-storage | | vcf_sv_clinical_index, sv_annotated_ranked_filtered | True | vcf-sv-clinical-index | scout, clinical-delivery, long-term-storage | -| svs_per_caller, vcf_hificnv | True | hificnv, vcf | long-term-storage | -| svs_per_caller, vcf_hificnv_index | True | hificnv, vcf-index | long-term-storage | -| svs_per_caller, vcf_sawfish | True | sawfish, vcf | long-term-storage | -| svs_per_caller, vcf_sawfish_index | True | sawfish, vcf-index | long-term-storage | -| svs_per_caller, vcf_severus | True | severus, vcf | long-term-storage | -| svs_per_caller, vcf_severus_index | True | severus, vcf-index | long-term-storage | +| svs_per_caller, vcf_hificnv | False | hificnv, vcf | long-term-storage | +| svs_per_caller, vcf_hificnv_index | False | hificnv, vcf-index | long-term-storage | +| svs_per_caller, vcf_sawfish | False | sawfish, vcf | long-term-storage | +| svs_per_caller, vcf_sawfish_index | False | sawfish, vcf-index | long-term-storage | +| svs_per_caller, vcf_severus | False | severus, vcf | long-term-storage | +| svs_per_caller, vcf_severus_index | False | severus, vcf-index | long-term-storage | | svs_per_caller, vcf_sniffles | True | sniffles1, vcf | long-term-storage | | svs_per_caller, vcf_sniffles_index | True | sniffles1, vcf-index | long-term-storage | | copy_number, bedgraph | True | cnv, bedgraph | clinical-delivery, long-term-storage | From 92db1fdf9c82244b52e3863c70989405b37626db Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Jul 2026 09:41:16 +0200 Subject: [PATCH 4/6] whatshap optional --- cg_hermes/config/nallo.py | 6 +++--- docs/nallo_map.md | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cg_hermes/config/nallo.py b/cg_hermes/config/nallo.py index dc53bd6..b4ba9c9 100644 --- a/cg_hermes/config/nallo.py +++ b/cg_hermes/config/nallo.py @@ -338,7 +338,7 @@ }, 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"]): { @@ -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"}): { diff --git a/docs/nallo_map.md b/docs/nallo_map.md index 91a16f3..832b567 100644 --- a/docs/nallo_map.md +++ b/docs/nallo_map.md @@ -62,7 +62,7 @@ | svs_per_caller, vcf_severus_index | False | severus, vcf-index | long-term-storage | | svs_per_caller, vcf_sniffles | True | sniffles1, vcf | long-term-storage | | svs_per_caller, vcf_sniffles_index | True | sniffles1, vcf-index | long-term-storage | -| copy_number, bedgraph | True | cnv, bedgraph | clinical-delivery, long-term-storage | +| copy_number, bedgraph | False | cnv, bedgraph | clinical-delivery, long-term-storage | | depth_track, bigwig | True | hificnv, bigwig | clinical-delivery, long-term-storage | | maf_depth_track, bigwig | True | hificnv, bigwig, maf | clinical-delivery, long-term-storage | | multiqc-json, multiqc | True | multiqc-json | long-term-storage | @@ -71,8 +71,8 @@ | samplesheet | True | nextflow-samplesheet | cg, long-term-storage | | software-versions | True | software-versions | cg, clinical-delivery, long-term-storage | | qc-metrics | True | qc-metrics, deliverable | cg, long-term-storage | -| whatshap, gtf | True | bam, paraphase | scout, clinical-delivery, long-term-storage | -| whatshap, gtf_index | True | bam, paraphase | scout, clinical-delivery, long-term-storage | +| whatshap, gtf | False | bam, paraphase | scout, clinical-delivery, long-term-storage | +| whatshap, gtf_index | False | bam, paraphase | scout, clinical-delivery, long-term-storage | | manifest | False | manifest | scout, long-term-storage | | chromograph_rhoviz, autozyg | False | chromograph, autozyg | scout | | tcov, chromograph_cov | False | chromograph, tcov | scout From 662bd58b9244d777a3acc695ddd965395ee49422 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Jul 2026 09:54:59 +0200 Subject: [PATCH 5/6] hificnv depth optional --- cg_hermes/config/nallo.py | 4 ++-- docs/nallo_map.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cg_hermes/config/nallo.py b/cg_hermes/config/nallo.py index b4ba9c9..9a8423d 100644 --- a/cg_hermes/config/nallo.py +++ b/cg_hermes/config/nallo.py @@ -343,12 +343,12 @@ }, 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"]): { diff --git a/docs/nallo_map.md b/docs/nallo_map.md index 832b567..ed9c6d5 100644 --- a/docs/nallo_map.md +++ b/docs/nallo_map.md @@ -63,8 +63,8 @@ | svs_per_caller, vcf_sniffles | True | sniffles1, vcf | long-term-storage | | svs_per_caller, vcf_sniffles_index | True | sniffles1, vcf-index | long-term-storage | | copy_number, bedgraph | False | cnv, bedgraph | clinical-delivery, long-term-storage | -| depth_track, bigwig | True | hificnv, bigwig | clinical-delivery, long-term-storage | -| maf_depth_track, bigwig | True | hificnv, bigwig, maf | clinical-delivery, long-term-storage | +| depth_track, bigwig | False | hificnv, bigwig | clinical-delivery, long-term-storage | +| maf_depth_track, bigwig | False | hificnv, bigwig, maf | clinical-delivery, long-term-storage | | multiqc-json, multiqc | True | multiqc-json | long-term-storage | | nextflow-params | True | nextflow-params | cg, long-term-storage | | nextflow-config | True | nextflow-config | cg, long-term-storage | From 41f19d1f9495885e344f31ce4b6211520dc73e8a Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 31 Jul 2026 09:10:10 +0200 Subject: [PATCH 6/6] pedigree optional --- cg_hermes/config/nallo.py | 2 +- docs/nallo_map.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cg_hermes/config/nallo.py b/cg_hermes/config/nallo.py index 9a8423d..fe60e60 100644 --- a/cg_hermes/config/nallo.py +++ b/cg_hermes/config/nallo.py @@ -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"]): { diff --git a/docs/nallo_map.md b/docs/nallo_map.md index ed9c6d5..a090b35 100644 --- a/docs/nallo_map.md +++ b/docs/nallo_map.md @@ -25,7 +25,7 @@ | methbat_profile, methylation_calling | False | methylation-tsv, methbat-profile | scout, clinical-delivery, long-term-storage | | mosdepth_d4, qc_bam | False | coverage, d4 | scout, clinical-delivery, long-term-storage | | multiqc-html, multiqc | True | multiqc-html | scout, clinical-delivery, long-term-storage | -| pedigree_fam, pedigree | True | pedigree | clinical-delivery, scout, long-term-storage | +| pedigree_fam, pedigree | False | pedigree | clinical-delivery, scout, long-term-storage | | relate_html, somalier | True | somalier, relate-html | clinical-delivery, scout, long-term-storage | | relate_pairs, somalier | True | somalier, relate-pairs | scout, long-term-storage | | relate_samples, somalier | True | somalier, relate-samples | scout, long-term-storage |