Mercurial > repos > rnateam > peakachu

diff peakachu.xml @ 3:886f5adba83d draft

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planemo upload for repository https://github.com/tbischler/PEAKachu commit 4a5c3c370df53a00aded3eaae40f3a8e4a263385-dirty
author rnateam
date Mon, 04 Feb 2019 13:04:19 -0500
parents 49a5a2e86c84
children 940b1d632f4d
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line diff
--- 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