broadinstitute · epiercehoffman · Oct 29, 2024 · Oct 17, 2024 · Oct 17, 2024 · Oct 17, 2024
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
@@ -4,7 +4,7 @@ workflows:
     name: GatherSampleEvidence
     primaryDescriptorPath: /wdl/GatherSampleEvidence.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -13,7 +13,7 @@ workflows:
     name: EvidenceQC
     primaryDescriptorPath: /wdl/EvidenceQC.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -22,7 +22,7 @@ workflows:
     name: TrainGCNV
     primaryDescriptorPath: /wdl/TrainGCNV.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -31,7 +31,7 @@ workflows:
     name: GatherBatchEvidence
     primaryDescriptorPath: /wdl/GatherBatchEvidence.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -40,7 +40,7 @@ workflows:
     name: ClusterBatch
     primaryDescriptorPath: /wdl/ClusterBatch.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -49,7 +49,7 @@ workflows:
     name: GenerateBatchMetrics
     primaryDescriptorPath: /wdl/GenerateBatchMetrics.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -58,7 +58,7 @@ workflows:
     name: FilterBatchSites
     primaryDescriptorPath: /wdl/FilterBatchSites.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -67,7 +67,7 @@ workflows:
     name: PlotSVCountsPerSample
     primaryDescriptorPath: /wdl/PlotSVCountsPerSample.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -76,7 +76,7 @@ workflows:
     name: FilterBatchSamples
     primaryDescriptorPath: /wdl/FilterBatchSamples.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -85,7 +85,7 @@ workflows:
     name: MergeBatchSites
     primaryDescriptorPath: /wdl/MergeBatchSites.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -94,7 +94,7 @@ workflows:
     name: GenotypeBatch
     primaryDescriptorPath: /wdl/GenotypeBatch.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -103,7 +103,7 @@ workflows:
     name: RegenotypeCNVs
     primaryDescriptorPath: /wdl/RegenotypeCNVs.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -112,7 +112,7 @@ workflows:
     name: CombineBatches
     primaryDescriptorPath: /wdl/CombineBatches.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -121,7 +121,7 @@ workflows:
     name: ResolveComplexVariants
     primaryDescriptorPath: /wdl/ResolveComplexVariants.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -130,7 +130,7 @@ workflows:
     name: GenotypeComplexVariants
     primaryDescriptorPath: /wdl/GenotypeComplexVariants.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -139,7 +139,43 @@ workflows:
     name: CleanVcf
     primaryDescriptorPath: /wdl/CleanVcf.wdl
     filters:
-      branches: 
+      branches:
+        - main
+      tags:
+        - /.*/
+
+  - subclass: WDL
+    name: RefineComplexVariants
+    primaryDescriptorPath: /wdl/RefineComplexVariants.wdl
+    filters:
+      branches:
+        - main
+      tags:
+        - /.*/
+
+  - subclass: WDL
+    name: JoinRawCalls
+    primaryDescriptorPath: /wdl/JoinRawCalls.wdl
+    filters:
+      branches:
+        - main
+      tags:
+        - /.*/
+
+  - subclass: WDL
+    name: SVConcordance
+    primaryDescriptorPath: /wdl/SVConcordance.wdl
+    filters:
+      branches:
+        - main
+      tags:
+        - /.*/
+
+  - subclass: WDL
+    name: FilterGenotypes
+    primaryDescriptorPath: /wdl/FilterGenotypes.wdl
+    filters:
+      branches:
         - main
       tags:
         - /.*/
@@ -148,7 +184,7 @@ workflows:
     name: MainVcfQc
     primaryDescriptorPath: /wdl/MainVcfQc.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/
@@ -157,7 +193,7 @@ workflows:
     name: AnnotateVcf
     primaryDescriptorPath: /wdl/AnnotateVcf.wdl
     filters:
-      branches: 
+      branches:
         - main
       tags:
         - /.*/

diff --git a/README.md b/README.md
@@ -27,4 +27,4 @@ continuous integration (CI) and continuous delivery (CD).
 GATK-SV CI/CD is developed as a set of Github Actions
 workflows that are available under the `.github/workflows`
 directory. Please refer to the [workflow's README](.github/workflows/README.md) 
-for their current coverage and setup. 
+for their current coverage and setup. 
diff --git a/inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl b/inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl
@@ -61,10 +61,11 @@ The following workflows are included in this workspace, to be executed in this o
 13. `13-ResolveComplexVariants`: Complex variant resolution
 14. `14-GenotypeComplexVariants`: Complex variant re-genotyping
 15. `15-CleanVcf`: VCF cleanup
-16. `16-JoinRawCalls`: Combines unfiltered calls (from step 5) across batches
-17. `17-SVConcordance`: Annotates variants with genotype concordance against raw calls
-18. `18-FilterGenotypes`: Performs genotype filtering to improve precision and generates QC plots
-19. `19-AnnotateVcf`: Cohort VCF annotations, including functional annotation, allele frequency (AF) annotation, and AF annotation with external population callsets
+16. `16-RefineComplexVariants`: Complex variant and translocation refinement
+17. `17-JoinRawCalls`: Combines unfiltered calls (from step 5) across batches
+18. `18-SVConcordance`: Annotates variants with genotype concordance against raw calls
+19. `19-FilterGenotypes`: Performs genotype filtering to improve precision and generates QC plots
+20. `20-AnnotateVcf`: Cohort VCF annotations, including functional annotation, allele frequency (AF) annotation, and AF annotation with external population callsets
 
 Additional downstream modules, such as those for visualization, are under development. They are not included in this workspace at this time, but the source code can be found in the [GATK-SV GitHub repository](https://github.com/broadinstitute/gatk-sv). See **Downstream steps** towards the bottom of this page for more information.
 
@@ -205,9 +206,9 @@ Read the full MergeBatchSites documentation [here](https://github.com/broadinsti
 Read the full GenotypeBatch documentation [here](https://github.com/broadinstitute/gatk-sv#genotype-batch).
 * Use the same `sample_set` definitions you used for `03-TrainGCNV` through `08-FilterBatchSamples`.
 
-#### 11-RegenotypeCNVs, 12-CombineBatches, 13-ResolveComplexVariants, 14-GenotypeComplexVariants, 15-CleanVcf, 16-JoinRawCalls, 17-SVConcordance, 18-FilterGenotypes, and 19-AnnotateVcf
+#### 11-RegenotypeCNVs, 12-CombineBatches, 13-ResolveComplexVariants, 14-GenotypeComplexVariants, 15-CleanVcf, 16-RefineComplexVariants, 17-JoinRawCalls, 18-SVConcordance, 19-FilterGenotypes, and 20-AnnotateVcf
 
-Read the full documentation for [RegenotypeCNVs](https://github.com/broadinstitute/gatk-sv#regenotype-cnvs), [MakeCohortVcf](https://github.com/broadinstitute/gatk-sv#make-cohort-vcf) (which includes `CombineBatches`, `ResolveComplexVariants`, `GenotypeComplexVariants`, `CleanVcf`), [`JoinRawCalls`](https://github.com/broadinstitute/gatk-sv#join-raw-calls), [`SVConcordance`](https://github.com/broadinstitute/gatk-sv#svconcordance), [`FilterGenotypes`](https://github.com/broadinstitute/gatk-sv#filter-genotypes), and [AnnotateVcf](https://github.com/broadinstitute/gatk-sv#annotate-vcf) on the README.
+Read the full documentation for [RegenotypeCNVs](https://github.com/broadinstitute/gatk-sv#regenotype-cnvs), [MakeCohortVcf](https://github.com/broadinstitute/gatk-sv#make-cohort-vcf) (which includes `CombineBatches`, `ResolveComplexVariants`, `GenotypeComplexVariants`, `CleanVcf`), [`RefineComplexVariants`](https://github.com/broadinstitute/gatk-sv#refine-complex), [`JoinRawCalls`](https://github.com/broadinstitute/gatk-sv#join-raw-calls), [`SVConcordance`](https://github.com/broadinstitute/gatk-sv#svconcordance), [`FilterGenotypes`](https://github.com/broadinstitute/gatk-sv#filter-genotypes), and [AnnotateVcf](https://github.com/broadinstitute/gatk-sv#annotate-vcf) on the README.
 * Use the same cohort `sample_set_set` you created and used for `09-MergeBatchSites`.
 
 #### Downstream steps

diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl
@@ -1,6 +1,8 @@
 {
   "CleanVcf.contig_list": "${workspace.primary_contigs_fai}",
   "CleanVcf.allosome_fai": "${workspace.allosome_file}",
+  "CleanVcf.HERVK_reference": "${workspace.HERVK_reference}",
+  "CleanVcf.LINE1_reference": "${workspace.LINE1_reference}",
   "CleanVcf.chr_x": "${workspace.chr_x}",
   "CleanVcf.chr_y": "${workspace.chr_y}",
 

diff --git a/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl b/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl
@@ -8,6 +8,8 @@
   "MakeCohortVcf.depth_exclude_list": "${workspace.depth_exclude_list}",
   "MakeCohortVcf.empty_file" : "${workspace.empty_file}",
   "MakeCohortVcf.ref_dict": "${workspace.reference_dict}",
+  "MakeCohortVcf.HERVK_reference": "${workspace.HERVK_reference}",
+  "MakeCohortVcf.LINE1_reference": "${workspace.LINE1_reference}",
 
   "MakeCohortVcf.site_level_comparison_datasets": [
     {{ reference_resources.ccdg_abel_site_level_benchmarking_dataset | tojson }},

diff --git a/...ates/terra_workspaces/cohort_mode/workflow_configurations/RefineComplexVariants.json.tmpl b/...ates/terra_workspaces/cohort_mode/workflow_configurations/RefineComplexVariants.json.tmpl
@@ -0,0 +1,17 @@
+{
+  "RefineComplexVariants.vcf": "${this.cleaned_vcf}",
+  "RefineComplexVariants.prefix": "${this.sample_set_set_id}",
+
+  "RefineComplexVariants.batch_name_list": "${this.sample_sets.sample_set_id}",
+  "RefineComplexVariants.batch_sample_lists": "${this.sample_sets.filtered_batch_samples_file}",
+  "RefineComplexVariants.PE_metrics": "${this.sample_sets.merged_PE}",
+  "RefineComplexVariants.PE_metrics_indexes": "${this.sample_sets.merged_PE_index}",
+  "RefineComplexVariants.Depth_DEL_beds": "${this.sample_sets.merged_dels}",
+  "RefineComplexVariants.Depth_DUP_beds": "${this.sample_sets.merged_dups}",
+
+  "RefineComplexVariants.n_per_split": "15000",
+
+  "RefineComplexVariants.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
+  "RefineComplexVariants.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
+  "RefineComplexVariants.linux_docker": "${workspace.linux_docker}"
+}
diff --git a/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/SVConcordance.json.tmpl b/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/SVConcordance.json.tmpl
@@ -2,7 +2,7 @@
   "SVConcordance.gatk_docker": "${workspace.gatk_docker}",
   "SVConcordance.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
 
-  "SVConcordance.eval_vcf" : "${this.cleaned_vcf}",
+  "SVConcordance.eval_vcf" : "${this.cpx_refined_vcf}",
   "SVConcordance.truth_vcf" : "${this.joined_raw_calls_vcf}",
 
   "SVConcordance.output_prefix": "${this.sample_set_set_id}",

diff --git a/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl
@@ -29,6 +29,8 @@ exclude_intervals_for_gcnv_filter_intervals	{{ reference_resources.exclude_inter
 external_af_ref_bed	{{ reference_resources.external_af_ref_bed }}
 external_af_ref_bed_prefix	{{ reference_resources.external_af_ref_bed_prefix }}
 genome_file	{{ reference_resources.genome_file }}
+HERVK_reference	{{ reference_resources.hervk_reference }}
+LINE1_reference	{{ reference_resources.line1_reference }}
 manta_region_bed	{{ reference_resources.manta_region_bed }}
 manta_region_bed_index	{{ reference_resources.manta_region_bed_index }}
 mei_bed	{{ reference_resources.mei_bed }}

diff --git a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.json.tmpl
@@ -97,6 +97,9 @@
   "GATKSVPipelineSingleSample.clean_vcf_random_seed": 0,
   "GATKSVPipelineSingleSample.run_vcf_qc" : false,
 
+  "GATKSVPipelineSingleSample.MakeCohortVcf.HERVK_reference": "${workspace.reference_HERVK}",
+  "GATKSVPipelineSingleSample.MakeCohortVcf.LINE1_reference": "${workspace.reference_LINE1}",
+
   "GATKSVPipelineSingleSample.protein_coding_gtf" : "${workspace.reference_protein_coding_gtf}",
   "GATKSVPipelineSingleSample.noncoding_bed" :       "${workspace.reference_noncoding_bed}",
   "GATKSVPipelineSingleSample.external_af_ref_bed" :       "${workspace.reference_external_af_ref_bed}",

diff --git a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl
@@ -55,6 +55,8 @@ reference_exclude_intervals_for_gcnv_filter_intervals	{{ reference_resources.exc
 reference_external_af_ref_bed	{{ reference_resources.external_af_ref_bed }}
 reference_external_af_ref_bed_prefix	{{ reference_resources.external_af_ref_bed_prefix }}
 reference_genome_file	{{ reference_resources.genome_file }}
+reference_HERVK	{{ reference_resources.hervk_reference }}
+reference_LINE1	{{ reference_resources.line1_reference }}
 reference_manta_region_bed	{{ reference_resources.manta_region_bed }}
 reference_manta_region_bed_index	{{ reference_resources.manta_region_bed_index }}
 reference_mei_bed	{{ reference_resources.mei_bed }}

diff --git a/inputs/templates/test/FilterGenotypes/FilterGenotypes.fixed_cutoffs.json.tmpl b/inputs/templates/test/FilterGenotypes/FilterGenotypes.fixed_cutoffs.json.tmpl
@@ -5,7 +5,13 @@
   "FilterGenotypes.gq_recalibrator_model_file": {{ reference_resources.aou_recalibrate_gq_model_file | tojson }},
   "FilterGenotypes.sl_filter_args": "--small-del-threshold 93 --medium-del-threshold 150 --small-dup-threshold -51 --medium-dup-threshold -4 --ins-threshold -13 --inv-threshold -19",
 
-  "FilterGenotypes.genome_tracks": {{ reference_resources.recalibrate_gq_genome_tracks | tojson }},
+  "FilterGenotypes.genome_tracks": [
+    {{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_simple_repeats | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_umap100 | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_umap24 | tojson }}
+  ],
   "FilterGenotypes.recalibrate_gq_args": [
     "--keep-homvar false",
     "--keep-homref true",

diff --git a/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl b/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl
@@ -6,7 +6,13 @@
 
   "FilterGenotypes.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
   "FilterGenotypes.gq_recalibrator_model_file": {{ reference_resources.aou_recalibrate_gq_model_file | tojson }},
-  "FilterGenotypes.genome_tracks": {{ reference_resources.recalibrate_gq_genome_tracks | tojson }},
+  "FilterGenotypes.genome_tracks": [
+    {{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_simple_repeats | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_umap100 | tojson }},
+    {{ reference_resources.recalibrate_gq_genome_track_umap24 | tojson }}
+  ],
   "FilterGenotypes.recalibrate_gq_args": [
     "--keep-homvar false",
     "--keep-homref true",

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl
@@ -134,6 +134,8 @@
   "GATKSVPipelineBatch.MakeCohortVcf.mei_bed": {{ reference_resources.mei_bed | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.pe_exclude_list": {{ reference_resources.pesr_exclude_list | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.depth_exclude_list": {{ reference_resources.depth_exclude_list | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.HERVK_reference": {{ reference_resources.hervk_reference | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.LINE1_reference": {{ reference_resources.line1_reference | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.min_sr_background_fail_batches": 0.5,
   "GATKSVPipelineBatch.MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
   "GATKSVPipelineBatch.MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl
@@ -127,6 +127,8 @@
   "GATKSVPipelineBatch.MakeCohortVcf.mei_bed": {{ reference_resources.mei_bed | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.pe_exclude_list": {{ reference_resources.pesr_exclude_list | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.depth_exclude_list": {{ reference_resources.depth_exclude_list | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.HERVK_reference": {{ reference_resources.hervk_reference | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.LINE1_reference": {{ reference_resources.line1_reference | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.min_sr_background_fail_batches": 0.5,
   "GATKSVPipelineBatch.MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
   "GATKSVPipelineBatch.MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,

diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
@@ -101,6 +101,9 @@
   "GATKSVPipelineSingleSample.clean_vcf5_records_per_shard": 5000,
   "GATKSVPipelineSingleSample.run_vcf_qc" : false,
 
+  "GATKSVPipelineSingleSample.MakeCohortVcf.HERVK_reference": {{ reference_resources.hervk_reference | tojson }},
+  "GATKSVPipelineSingleSample.MakeCohortVcf.LINE1_reference": {{ reference_resources.line1_reference | tojson }},
+
   "GATKSVPipelineSingleSample.protein_coding_gtf" : {{ reference_resources.protein_coding_gtf | tojson }},
   "GATKSVPipelineSingleSample.noncoding_bed" :       {{ reference_resources.noncoding_bed | tojson }},
   "GATKSVPipelineSingleSample.external_af_ref_bed" :       {{ reference_resources.external_af_ref_bed | tojson }},

diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.melt.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.melt.json.tmpl
@@ -90,6 +90,10 @@
   "GATKSVPipelineSingleSample.depth_clustering_algorithm": "SINGLE_LINKAGE",
 
   "GATKSVPipelineSingleSample.ref_copy_number_autosomal_contigs" : 2,
+
+  "GATKSVPipelineSingleSample.MakeCohortVcf.HERVK_reference": {{ reference_resources.hervk_reference | tojson }},
+  "GATKSVPipelineSingleSample.MakeCohortVcf.LINE1_reference": {{ reference_resources.line1_reference | tojson }},
+
   "GATKSVPipelineSingleSample.clean_vcf_min_sr_background_fail_batches": 0.5,
   "GATKSVPipelineSingleSample.max_shard_size_resolve" : 500,
   "GATKSVPipelineSingleSample.clean_vcf_max_shards_per_chrom_clean_vcf_step1": 200,

diff --git a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl
@@ -1,6 +1,8 @@
 {
   "CleanVcf.contig_list": {{ reference_resources.primary_contigs_fai | tojson }},
   "CleanVcf.allosome_fai": {{ reference_resources.allosome_file | tojson }},
+  "CleanVcf.HERVK_reference": {{ reference_resources.hervk_reference | tojson }},
+  "CleanVcf.LINE1_reference": {{ reference_resources.line1_reference | tojson }},
   "CleanVcf.chr_x": {{ reference_resources.chr_x | tojson }},
   "CleanVcf.chr_y": {{ reference_resources.chr_y | tojson }},
 

diff --git a/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl
@@ -8,6 +8,8 @@
   "MakeCohortVcf.depth_exclude_list": {{ reference_resources.depth_exclude_list | tojson }},
   "MakeCohortVcf.empty_file" : {{ reference_resources.empty_file | tojson }},
   "MakeCohortVcf.ref_dict": {{ reference_resources.reference_dict | tojson }},
+  "MakeCohortVcf.HERVK_reference": {{ reference_resources.hervk_reference | tojson }},
+  "MakeCohortVcf.LINE1_reference": {{ reference_resources.line1_reference | tojson }},
 
   "MakeCohortVcf.site_level_comparison_datasets": [
     {{ reference_resources.ccdg_abel_site_level_benchmarking_dataset | tojson }},