Rank variants mivmir gicam test data

README.md

@@ -22,6 +22,15 @@ This branch contains test data to be used for automated testing with the [nf-cor
 
 `reference/mobile_elemement_references.tsv`: tsv file with paths to the mobile element locations on chromosome 21
 
+### For SNV subworkflow, scoring variants with MIVMIR, GICAM
+`reference/rank_model_dummy_mivmir_gicam_unit_test.ini`: Dummy genmod config for running genmod scoring
+
+`testdata/justhusky_snv_rank_variants_mivmir_gicam.vcf`: Data for running `rank_variants` subworkflow with MIVMIR, GICAM
+
+`testdata/justhusky_snv_mivmir.vcf`: Data for running MIVMIR module test
+
+`testdata/justhusky_snv_gicam.vcf`: Data for running GICAM module test
+
 ### For Mitochondrial subworkflow
 
 `reference/Homo_sapiens_assembly38_chr20_chrM.fasta`: chr20 and chrM hg38 reference fasta file

reference/rank_model_dummy_mivmir_gicam_unit_test.ini

@@ -0,0 +1,337 @@
+[Version]
+  version = 1.34
+  name = rank_model
+
+[Categories]
+  [[allele_frequency]]
+    category_aggregation = min
+
+ [[protein_prediction]]
+   category_aggregation = sum
+
+ [[gene_intolerance_prediction]]
+   category_aggregation = max
+
+ [[inheritance_models]]
+   category_aggregation = min
+
+ [[consequence]]
+   category_aggregation = max
+
+ [[conservation]]
+   category_aggregation = sum
+
+ [[variant_call_quality_filter]]
+   category_aggregation = sum
+
+ [[deleteriousness]]
+   category_aggregation = max
+
+ [[clinical_significance]]
+   category_aggregation = sum
+
+ [[splicing]]
+   category_aggregation = max
+
+[model_score]
+  category = variant_call_quality_filter
+  data_type = integer
+  description = Inheritance model score
+  field = INFO
+  info_key = ModelScore
+  record_rule = min
+  separators = ',',':',
+
+  [[not_reported]]
+    score = 0
+
+  [[low_qual]]
+    score = -5
+    lower = 0
+    upper = 10
+
+  [[medium_qual]]
+    score = -2
+    lower = 10
+    upper = 20
+
+  [[high_qual]]
+    score = 0
+    lower = 20
+    upper = 300
+
+[genetic_models]
+  category = inheritance_models
+  data_type = string
+  description = Inheritance models followed for the variant
+  field = INFO
+  info_key = GeneticModels
+  record_rule = max
+  separators = ',', ':', '|',
+
+ [[ad]]
+   priority = 1
+   score = 1
+   string = 'AD'
+
+ [[ad_dn]]
+   score = 1
+   priority = 1
+   string = 'AD_dn'
+
+ [[ar]]
+   score = 1
+   priority = 1
+   string = 'AR_hom'
+
+ [[ar_dn]]
+   score = 1
+   priority = 1
+   string = 'AR_hom_dn'
+
+ [[ar_comp]]
+   score = 1
+   priority = 1
+   string = 'AR_comp'
+
+ [[ar_comp_dn]]
+   score = 1
+   priority = 1
+   string = 'AR_comp_dn'
+
+ [[xr]]
+   score = 1
+   priority = 1
+   string = 'XR'
+
+ [[xr_dn]]
+   score = 1
+   priority = 1
+   string = 'XR_dn'
+
+ [[xd]]
+   score = 1
+   priority = 1
+   string = 'XD'
+
+ [[xd_dn]]
+   score = 1
+   priority = 1
+   string = 'XD_dn'
+
+ [[not_reported]]
+   score = -12
+
+[most_severe_consequence]
+  category = consequence
+  data_type = string
+  description = Most severe consequence for this variant
+  field = INFO
+  info_key = most_severe_consequence
+  record_rule = max
+  separators = ',', ':', '|',
+
+  [[transcript_ablation]]
+    score = 10
+    priority = 6
+    string = 'transcript_ablation'
+
+  [[initiator_codon_variant]]
+    score = 9
+    priority = 5
+    string = 'initiator_codon_variant'
+
+  [[frameshift_variant]]
+    score = 8
+    priority = 5
+    string = 'frameshift_variant'
+
+  [[stop_gained]]
+    score = 8
+    priority = 5
+    string = 'stop_gained'
+
+  [[start_lost]]
+    score = 8
+    priority = 5
+    string = 'start_lost'
+
+  [[stop_lost]]
+    score = 8
+    priority = 5
+    string = 'stop_lost'
+
+  [[splice_acceptor_variant]]
+    score = 8
+    priority = 5
+    string = 'splice_acceptor_variant'
+
+  [[splice_donor_variant]]
+    score = 8
+    priority = 5
+    string = 'splice_donor_variant'
+
+  [[inframe_deletion]]
+    score = 5
+    priority = 4
+    string = 'inframe_deletion'
+
+  [[transcript_amplification]]
+    score = 5
+    priority = 4
+    string = 'transcript_amplification'
+
+  [[splice_region_variant]]
+    score = 5
+    priority = 4
+    string = 'splice_region_variant'
+
+  [[missense_variant]]
+    score = 5
+    priority = 4
+    string = 'missense_variant'
+
+  [[protein_altering_variant]]
+    score = 5
+    priority = 4
+    string = 'protein_altering_variant'
+
+  [[inframe_insertion]]
+    score = 5
+    priority = 4
+    string = 'inframe_insertion'
+
+  [[incomplete_terminal_codon_variant]]
+    score = 5
+    priority = 4
+    string = 'incomplete_terminal_codon_variant'
+
+  [[non_coding_transcript_exon_variant]]
+    score = 3
+    priority = 2
+    string = 'non_coding_transcript_exon_variant'
+
+  [[synonymous_variant]]
+    score = 2
+    priority = 2
+    string = 'synonymous_variant'
+
+  [[mature_mirna_variant]]
+    score = 1
+    priority = 2
+    string = 'mature_mirna_variant'
+
+  [[non_coding_transcript_variant]]
+    score = 1
+    priority = 2
+    string = 'non_coding_transcript_variant'
+
+  [[regulatory_region_variant]]
+    score = 1
+    priority = 2
+    string = 'regulatory_region_variant'
+
+  [[upstream_gene_variant]]
+    score = 1
+    priority = 2
+    string = 'upstream_gene_variant'
+
+  [[regulatory_region_amplification]]
+    score = 1
+    priority = 2
+    string = 'regulatory_region_amplification'
+
+  [[tfbs_amplification]]
+    score = 1
+    priority = 2
+    string = 'tfbs_amplification'
+
+  [[5_prime_utr_variant]]
+    score = 1
+    priority = 2
+    string = '5_prime_utr_variant'
+
+  [[intron_variant]]
+    score = 1
+    priority = 2
+    string = 'intron_variant'
+
+  [[3_prime_utr_variant]]
+    score = 1
+    priority = 2
+    string = '3_prime_utr_variant'
+
+  [[feature_truncation]]
+    score = 1
+    priority = 2
+    string = 'feature_truncation'
+
+  [[TF_binding_site_variant]]
+    score = 1
+    priority = 2
+    string = 'TF_binding_site_variant'
+
+  [[stop_retained_variant]]
+    score = 1
+    priority = 2
+    string = 'stop_retained_variant'
+
+  [[feature_elongation]]
+    score = 1
+    priority = 2
+    string = 'feature_elongation'
+
+  [[regulatory_region_ablation]]
+    score = 1
+    priority = 2
+    string = 'regulatory_region_ablation'
+
+  [[tfbs_ablation]]
+    score = 1
+    priority = 2
+    string = 'tfbs_ablation'
+
+  [[coding_sequence_variant]]
+    score = 1
+    priority = 2
+    string = 'coding_sequence_variant'
+
+  [[downstream_gene_variant]]
+    score = 1
+    priority = 2
+    string = 'downstream_gene_variant'
+
+  [[NMD_transcript_variant]]
+    score = 1
+    priority = 2
+    string = 'NMD_transcript_variant'
+
+  [[intergenic_variant]]
+    score = 0
+    priority = 0
+    string = 'intergenic_variant'
+
+  [[not_reported]]
+    score = 0
+
+[filter]
+  category = variant_call_quality_filter
+  data_type = string
+  description = The filters for the variant
+  field = FILTER
+  record_rule = min
+  separators = ';',
+
+  [[not_reported]]
+    score = 0
+
+  [[pass]]
+    score = 3
+    priority = 1
+    string = 'PASS'
+
+  [[dot]]
+    score = 3
+    priority = 2
+    string = '.'
+