Fix FilterGenotypes json template

broadinstitute · Jan 19, 2024 · 7944ad1 · 7944ad1
1 parent 693673d
commit 7944ad1
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl b/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl
@@ -4,33 +4,33 @@
   "FilterGenotypes.ploidy_table": {{ test_batch.ploidy_table | tojson }},
   "FilterGenotypes.truth_json": {{ test_batch.recalibrate_gq_truth_json | tojson }},
 
+  "FilterGenotypes.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
   "FilterGenotypes.gq_recalibrator_model_file": {{ reference_resources.aou_recalibrate_gq_model_file | tojson }},
-  "FilterGenotypes.RecalibrateGq.genome_tracks": {{ reference_resources.recalibrate_gq_genome_tracks | tojson }},
-  "FilterGenotypes.RecalibrateGq.recalibrate_gq_args": [
+  "FilterGenotypes.genome_tracks": {{ reference_resources.recalibrate_gq_genome_tracks | tojson }},
+  "FilterGenotypes.recalibrate_gq_args": [
     "--keep-homvar false",
     "--keep-homref true",
     "--keep-multiallelic true",
     "--skip-genotype-filtering true",
     "--min-samples-to-estimate-allele-frequency -1"
   ],
 
-  "FilterGenotypes.MainVcfQc.ped_file": {{ test_batch.ped_file | tojson }},
-  "FilterGenotypes.MainVcfQc.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
-  "FilterGenotypes.MainVcfQc.site_level_comparison_datasets": [
+  "FilterGenotypes.ped_file": {{ test_batch.ped_file | tojson }},
+  "FilterGenotypes.site_level_comparison_datasets": [
     {{ reference_resources.ccdg_abel_site_level_benchmarking_dataset | tojson }},
     {{ reference_resources.gnomad_v2_collins_site_level_benchmarking_dataset | tojson }},
     {{ reference_resources.hgsv_byrska_bishop_site_level_benchmarking_dataset | tojson }},
     {{ reference_resources.thousand_genomes_site_level_benchmarking_dataset | tojson }}
   ],
-  "FilterGenotypes.MainVcfQc.sample_level_comparison_datasets": [
+  "FilterGenotypes.sample_level_comparison_datasets": [
     {{ reference_resources.hgsv_byrska_bishop_sample_level_benchmarking_dataset | tojson }}
   ],
-  "FilterGenotypes.MainVcfQc.sample_renaming_tsv": {{ reference_resources.hgsv_byrska_bishop_sample_renaming_tsv | tojson }},
-  "FilterGenotypes.MainVcfQc.runtime_override_per_sample_benchmark_plot": {
+  "FilterGenotypes.sample_renaming_tsv": {{ reference_resources.hgsv_byrska_bishop_sample_renaming_tsv | tojson }},
+  "FilterGenotypes.runtime_override_per_sample_benchmark_plot": {
     "mem_gb": 30,
     "disk_gb": 50
   },
-  "FilterGenotypes.MainVcfQc.runtime_override_plot_qc_per_family": {
+  "FilterGenotypes.runtime_override_plot_qc_per_family": {
     "mem_gb": 15,
     "disk_gb": 100
   },