From 190d41d6a708cf0390a1689110bd83f1279e6732 Mon Sep 17 00:00:00 2001 From: jpsmith5 Date: Tue, 26 Mar 2019 11:25:24 -0400 Subject: [PATCH] fix whitespace issue with parameterization --- pipelines/pepatac.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipelines/pepatac.py b/pipelines/pepatac.py index e09798a0..38850575 100755 --- a/pipelines/pepatac.py +++ b/pipelines/pepatac.py @@ -173,7 +173,7 @@ def _align_with_bt2(args, tools, paired, useFIFO, unmap_fq1, unmap_fq2, if not bt2_opts_txt: # Default options - bt2_opts_txt = " -k 1" # Return only 1 alignment + bt2_opts_txt = "-k 1" # Return only 1 alignment bt2_opts_txt += " -D 20 -R 3 -N 1 -L 20 -i S,1,0.50" # samtools sort needs a temporary directory @@ -203,7 +203,7 @@ def _align_with_bt2(args, tools, paired, useFIFO, unmap_fq1, unmap_fq2, # Build bowtie2 command cmd = "(" + tools.bowtie2 + " -p " + str(pm.cores) - cmd += bt2_opts_txt + cmd += " " + bt2_opts_txt cmd += " -x " + assembly_bt2 cmd += " --rg-id " + args.sample_name cmd += " -U " + unmap_fq1