Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 90:6809c63d9161 draft

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"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
author rhpvorderman
date Tue, 25 Jan 2022 11:28:29 +0000
parents 3c9d4d976c47
children f387cc1580c6
comparison
equal deleted inserted replaced
89:3c9d4d976c47 90:6809c63d9161
893 IFS="$tIFS" 893 IFS="$tIFS"
894 894
895 echo "---------------- remove_files----------------" 895 echo "---------------- remove_files----------------"
896 echo "---------------- remove_files----------------<br />" >> $log 896 echo "---------------- remove_files----------------<br />" >> $log
897 897
898 rm -r -v -f results/baseline 898 rm -r -v -f $outdir/baseline
899 rm -r -v -f files 899 rm -r -v -f $PWD/files
900 filename='remove_files.txt' 900 rm -v $PWD/aa.txt
901 rm -v $PWD/aa_change_stats.txt
902 rm -v $PWD/gapped_aa.txt
903 rm -v $PWD/gapped_nt.txt
904 rm -v $PWD/hotspots.txt
905 rm -v $PWD/junction.txt
906 rm -v $PWD/mutationanalysis.txt
907 rm -v $PWD/mutationstats.txt
908 rm -v $PWD/sequences.txt
909 rm -v $PWD/summary.txt
910 rm -v $PWD/Rplots.pdf
911
912 filename="$dir/remove_files.txt"
901 913
902 while read file; do 914 while read file; do
903 rm -v -f $file 915 rm -v -f $outdir/$file
904 done < "$filename" 916 done < "$filename"
905
906 917
907 echo "---------------- Done! ----------------" 918 echo "---------------- Done! ----------------"
908 echo "---------------- Done! ----------------<br />" >> $outdir/log.html 919 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
909 920
910 921