Commit 8c8f8e71 authored by Overduin, Sam's avatar Overduin, Sam
Browse files

Update reset_spades_for_taxa.sh

parent 23e87ed6
#!/bin/bash
# Author: Sam Overduin
spades_folder="$1"
spades_py_executable="/mnt/LTR_userdata/overd008/tools/bin/spades.py"
spades_folder="$1"
#cd "$spades_folder"
if [ "$2" == "barcode" ]; then
......@@ -14,8 +15,6 @@ 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 "$spades_folder"/pipeline_state/stage_5_as_finish
......@@ -26,12 +25,6 @@ rm "$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
......
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