From 039ae01862205b43ae69ca8e13ab4e6108fea8b3 Mon Sep 17 00:00:00 2001 From: bw2 Date: Wed, 7 Feb 2024 14:40:05 -0500 Subject: [PATCH] updated storage requirements for the realign_to_T2T example pipeline --- examples/realign_to_T2T.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/realign_to_T2T.py b/examples/realign_to_T2T.py index a225464..c9eeefe 100644 --- a/examples/realign_to_T2T.py +++ b/examples/realign_to_T2T.py @@ -56,7 +56,7 @@ def main(): # step 2: convert to fastq cpus = 1 s2 = batch_pipeline.new_step(f"fastq: {prefix}", step_number=2, arg_suffix="step2", - image=DOCKER_IMAGE, cpu=cpus, memory="standard", storage="200G", output_dir=args.output_dir) + image=DOCKER_IMAGE, cpu=cpus, memory="standard", storage="300G", output_dir=args.output_dir) s2.switch_gcloud_auth_to_user_account() local_bam_or_cram = s2.use_previous_step_outputs_as_inputs(s1) @@ -77,7 +77,7 @@ def main(): # step 3: align to T2T cpus = 8 s3 = batch_pipeline.new_step(f"bwa mem: {prefix}", step_number=3, arg_suffix="step3", - image=DOCKER_IMAGE, cpu=cpus, memory="standard", storage="200G", output_dir=args.output_dir) + image=DOCKER_IMAGE, cpu=cpus, memory="standard", storage="300G", output_dir=args.output_dir) s3.switch_gcloud_auth_to_user_account() local_r1_fastq, local_r2_fastq = s3.use_previous_step_outputs_as_inputs(s2, localize_by=Localize.COPY)