From b4cef84b41d9cb4e7d11c273468a91a288715335 Mon Sep 17 00:00:00 2001 From: iquasere Date: Mon, 14 Jun 2021 09:34:13 +0100 Subject: [PATCH] Another fix for trimmomatic --- workflow/scripts/preprocess.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/scripts/preprocess.py b/workflow/scripts/preprocess.py index 62edaa1..6cc691d 100644 --- a/workflow/scripts/preprocess.py +++ b/workflow/scripts/preprocess.py @@ -259,7 +259,7 @@ def quality_trimming(self, files, out_dir, name, threads='12', minlen='100', avg output_files = ' '.join([f'{out_dir}/Trimmomatic/quality_trimmed_{name}_{fr}_{pu}.fq' for fr in [ 'forward', 'reverse'] for pu in ['paired', 'unpaired']] ) if self.paired else f'{out_dir}/Trimmomatic/quality_trimmed_{name}.fq' - run_command(f"trimmomatic {'PE' if self.paired else 'SE'} -threads {threads} {' '.join(files)}" + run_command(f"trimmomatic {'PE' if self.paired else 'SE'} -threads {threads} {' '.join(files)} " f"{output_files}{f' CROP:{crop}' if crop < float('inf') else ''}" f"{f' HEADCROP:{headcrop}' if headcrop > 0 else ''}" f" AVGQUAL:{avgqual} MINLEN:{minlen}")