From 308b61b8c0f24ff9b0fdf98d1b4d02f42ef74a4b Mon Sep 17 00:00:00 2001 From: melissacline Date: Tue, 19 Dec 2023 22:24:01 -0800 Subject: [PATCH] Fixed a missing command line argument --- pipeline/splice_ai/add_spliceai_scores_for_new_variants.py | 2 +- pipeline/workflow/bayesdel_processing.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pipeline/splice_ai/add_spliceai_scores_for_new_variants.py b/pipeline/splice_ai/add_spliceai_scores_for_new_variants.py index 659875d2a..3184bbe8d 100644 --- a/pipeline/splice_ai/add_spliceai_scores_for_new_variants.py +++ b/pipeline/splice_ai/add_spliceai_scores_for_new_variants.py @@ -92,7 +92,7 @@ def main(): print(args.temp_dir) scored_vcf = args.temp_dir + "/scored_variants.vcf" unscored_vcf = args.temp_dir + "/unscored_variants.vcf" - newly_scored_vcf = args.temp_dir + "/newly_score_varaints.vcf" + newly_scored_vcf = args.temp_dir + "/newly_score_variants.vcf" shutil.copy2(args.scored_variants_vcf, scored_vcf) while not all_variants_scored: # diff --git a/pipeline/workflow/bayesdel_processing.py b/pipeline/workflow/bayesdel_processing.py index e4c640f64..1fd3c4276 100644 --- a/pipeline/workflow/bayesdel_processing.py +++ b/pipeline/workflow/bayesdel_processing.py @@ -47,7 +47,7 @@ def run(self): 'output/release/artifacts/variants_with_splice_ai.vcf') args = ["python", "add_splcieai_scores_for_new_variants.py", "-a", self.input().path, "-b", "1000", "-d", "4999", - "-f", brca_resources_dir + "/hg38.fa", "-f", "grch38", + "-f", brca_resources_dir + "/hg38.fa", "-g", "grch38", "-o", self.output().path, "-s", previous_vcf_path, "-t", tmp_dir] pipeline_utils.run_process(args)