From 07c49bf6fc93e8846e8826df63100a0b069cbe40 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Tue, 15 Sep 2020 12:27:36 +0200 Subject: [PATCH] Fix potential output name collisions (#117) --- OptiTypePipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/OptiTypePipeline.py b/OptiTypePipeline.py index 4e62ef6..8cfbc74 100755 --- a/OptiTypePipeline.py +++ b/OptiTypePipeline.py @@ -278,7 +278,7 @@ def get_num_threads(configured_threads): else: extension = 'sam' - bam_paths = args.input if bam_input else [os.path.join(out_dir, ("%s_%i.%s" % (date, i+1, extension))) for i in range(len(args.input))] + bam_paths = args.input if bam_input else [os.path.join(out_dir, ("%s_%i.%s" % (prefix, i+1, extension))) for i in range(len(args.input))] # SETUP variables and OUTPUT samples ref_type = "nuc" if args.rna else "gen"