Commit 6a5603c3 authored by peguerin's avatar peguerin
Browse files

script to clean outputs

parent 34141842
###############################################################################
MODE=$1
if [ -d "results" ]; then
if [ "$MODE" == "clear" ]; then
echo -n "Clearing..."
mv -i results cleared/
mkdir results
mkdir results/01_settings results/02_assembly results/03_demultiplex results/04_filter_samples results/05_assignment results/06_final_tables
mkdir results/02_assembly/01_illuminapairedend results/02_assembly/02_remove_unaligned
mkdir results/03_demultiplex/00_dat results/03_demultiplex/01_assign_sequences results/03_demultiplex/02_raw
mkdir results/04_filter_samples/01_dereplicated results/04_filter_samples/02_goodlength results/04_filter_samples/03_clean_pcrerr results/04_filter_samples/04_filtered
mkdir results/05_assignment/01_runs results/05_assignment/02_dereplicated results/05_assignment/03_assigned results/05_assignment/04_formated
echo "done"
elif [ "$MODE" == "reset" ]; then
echo -n "Resetting..."
rm -r results
mkdir results
mkdir results/01_settings results/02_assembly results/03_demultiplex results/04_filter_samples results/05_assignment results/06_final_tables
mkdir results/02_assembly/01_illuminapairedend results/02_assembly/02_remove_unaligned
mkdir results/03_demultiplex/00_dat results/03_demultiplex/01_assign_sequences results/03_demultiplex/02_raw
mkdir results/04_filter_samples/01_dereplicated results/04_filter_samples/02_goodlength results/04_filter_samples/03_clean_pcrerr results/04_filter_samples/04_filtered
mkdir results/05_assignment/01_runs results/05_assignment/02_dereplicated results/05_assignment/03_assigned results/05_assignment/04_formated
echo "done"
else
echo -n "You must set an action to perform:\n bash clean.sh clear "
else
echo "Cleaning is impossible... you are not in the right folder."
fi
\ No newline at end of file
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