diff --git a/scripts/reset_spades_for_taxa.sh b/scripts/reset_spades_for_taxa.sh index 077d4565842de8fe0c7937b29c288cf7beffd8ae..cbfc5cc66b904716f4af7c47fdd63a0ca8a7e3de 100644 --- a/scripts/reset_spades_for_taxa.sh +++ b/scripts/reset_spades_for_taxa.sh @@ -1,7 +1,8 @@ #!/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