From e114009c7bea991beb5de7a2e3a22c56341b548c Mon Sep 17 00:00:00 2001 From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:49:35 +1100 Subject: [PATCH] Update str/indel_locus_extractor.py Co-authored-by: Matt Welland --- str/indel_locus_extractor.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/str/indel_locus_extractor.py b/str/indel_locus_extractor.py index d6a1babe..813677ac 100644 --- a/str/indel_locus_extractor.py +++ b/str/indel_locus_extractor.py @@ -45,15 +45,8 @@ def indel_coordinate_extractor(file_path, gcs_path): @click.command() def main(file_path): - b = get_batch() - hail_job = b.new_python_job(name=f'Hail query filter for indels') - hail_job.image(config['workflow']['driver_image']) - hail_job.storage('20G') - hail_job.cpu(4) gcs_output_path = output_path(f'indels.tsv', 'analysis') - hail_job.call(indel_coordinate_extractor, file_path, gcs_output_path) - - b.run(wait=False) + indel_coordinate_extractor(file_path, gcs_output_path) if __name__ == '__main__':