env-template

REMOTE_PATH=/cfs/earth/scratch/voro/scripts

DATASET_NAME=Dataset_XY
DATA_PATH_IN=../data/Dataset_XY/
RUN_NAME_IN=RunName
RUN_NAME_OUT=RunName

FLOWCELL=FLO-FLG001
KIT=SQK-16S024

FILES_PER_SUBDIR=20

GUPPY_BASECALLER_PATH=../local_apps/ont-guppy-cpu/bin/guppy_basecaller

GUPPY_DEMULTIPLEXING_PATH=../local_apps/ont-guppy-cpu/bin//guppy_barcoder
QCAT_DEMULTIPLEXING_PATH=../python/bin/qcat

NANOFILT_QSCORE=7
NANOFILT_MIN_LENGTH=1000
NANOFILT_MAX_LENGTH=2000

PATH_KRAKEN2=../local_apps/kraken2/Kraken_Installation/kraken2 
PATH_KRAKEN2_DB_SILVA=../local_apps/kraken2/Kraken_Installation/SILVA/
PATH_KRAKEN2_DB_RDP=../local_apps/kraken2/Kraken_Installation/RDP/
PATH_KRAKEN2_DB_GG=../local_apps/kraken2/scripts/GREENGENES/

PATH_KRONATOOLS=../local_apps/krona/KronaTools-2.7.1/bin/bin/ktImportText
PATH_KRAKEN2KRONA=../local_apps/lskScripts/scripts/kraken2-translate.pl

UDOCKER_PATH=../local_apps/udocker