Merge pull request #1484 from BRCAChallenge/cleanup_spliceai

Fixed a missing command line argument
BRCAChallenge · Dec 20, 2023 · 45e9023 · 45e9023
2 parents 96f41d4 + f786757
commit 45e9023
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diff --git 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
@@ -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)