From 7944ad167b4f5165f6786b79dd002c7f86de26d8 Mon Sep 17 00:00:00 2001 From: Mark Walker Date: Fri, 19 Jan 2024 11:31:09 -0500 Subject: [PATCH] Fix FilterGenotypes json template --- .../FilterGenotypes.optimize_cutoffs.json.tmpl | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl b/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl index 6a249fa7d..dfeca6a72 100644 --- a/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl +++ b/inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl @@ -4,9 +4,10 @@ "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", @@ -14,23 +15,22 @@ "--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 },