Upload reset_spades_for_taxa.sh

scripts/reset_spades_for_taxa.sh

+#!/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