From f6ea096fa6e4a439d32bd934d4ad571eef0c5b40 Mon Sep 17 00:00:00 2001 From: Rachel LEGENDRE <rachel.legendre@pasteur.fr> Date: Wed, 10 Nov 2021 11:17:46 +0100 Subject: [PATCH] Update alienTrimmer.rules --- workflow/rules/alienTrimmer.rules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/alienTrimmer.rules b/workflow/rules/alienTrimmer.rules index 54004be..5be5250 100755 --- a/workflow/rules/alienTrimmer.rules +++ b/workflow/rules/alienTrimmer.rules @@ -59,7 +59,7 @@ rule alienTrimmer: # paired end or single end if [[ ${{#infiles[@]}} -eq 2 ]]; then - cmd+="-1 ${{infiles[0]}} -2 ${{infiles[1]}} -o out_paired" + cmd+=" -1 ${{infiles[0]}} -2 ${{infiles[1]}} -o out_paired" else cmd+=" -i ${{infiles[0]}} -o out_single" fi -- GitLab