Commit 48c747ea authored by Overduin, Sam's avatar Overduin, Sam
Browse files

Upload reset_spades_for_taxa.sh

parent 98bb1497
#!/bin/bash
spades_folder="$1"
#cd "$spades_folder"
if [ "$2" == "barcode" ]; then
rm -r "$spades_folder"/K55/saves/barcode_map_construction
echo "distance_estimation" > "$spades_folder"/K55/saves/checkpoint.dat
rm -r "$spades_folder/.bin_reads"
elif [ "$2" == "repeat" ]; then
echo "barcode_map_construction" > "$spades_folder"/K55/saves/checkpoint.dat
else
echo "$2 not found. Usage: reset_spades_for_taxa.sh spades-folder [barcode|repeat] ."
fi
spades_py_executable="$HOME/mnt/ltr/tools/taxa_spades_install_final/bin/spades.py"
rm "$spades_folder"/pipeline_state/stage_3_k55
rm "$spades_folder"/pipeline_state/stage_4_copy_files
rm "$spades_folder"/pipeline_state/stage_5_as_finish
rm "$spades_folder"/pipeline_state/stage_6_bs
rm "$spades_folder"/pipeline_state/stage_7_terminate
rm "$spades_folder"/pipeline_state/stage_7_k55
rm "$spades_folder"/pipeline_state/stage_8_copy_files
rm "$spades_folder"/pipeline_state/stage_9_as_finish
#overd008/both_norm/corrected/both_normalized
#overd008/both_norm_corrected_reads/both_normalized
#rm -r "$spades_folder"/K55/saves/barcode_map_construction
echo "Do you wish to continue the spades pipeline?
with: $spades_py_executable --continue -o $1 (y/n)"
read continue_pipeline
if [ "$continue_pipeline" == "y" ]; then
"$spades_py_executable" --continue -o "$1"
else
echo "done"
fi
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