Another fix for trimmomatic

iquasere · Jun 14, 2021 · b4cef84 · b4cef84
1 parent c49f892
commit b4cef84
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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}")