# HG changeset patch
# User rnateam
# Date 1549303459 18000
# Node ID 886f5adba83d1430996d07823bdb5e50023e52d2
# Parent  49a5a2e86c84c9eda63981e03047f592e4011ab5
planemo upload for repository https://github.com/tbischler/PEAKachu commit 4a5c3c370df53a00aded3eaae40f3a8e4a263385-dirty

diff -r 49a5a2e86c84 -r 886f5adba83d peakachu.xml
--- a/peakachu.xml	Wed Jan 16 17:52:56 2019 -0500
+++ b/peakachu.xml	Mon Feb 04 13:04:19 2019 -0500
@@ -68,10 +68,10 @@
         &&
         if ls ./tmp_output/peak_tables/*.csv > /dev/null;
         then 
-            cat ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
+            sed -n 1p ./tmp_output/peak_tables/*.csv > peaks.tsv &&
             tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
             mv peaks.tsv '$peak_tables' &&
-            cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
+            awk '/peak/ {print $0}' ./tmp_output/peak_annotations/*.gff > peak_annotations.gff &&
             mv peak_annotations.gff '$peak_annotations' &&
             mv ./tmp_output/plots/Initial*.png '$MA_plot';
         else