The env files contains all adjustable variables and paths. Depending on what kind of workflow or script the user wants to execute, certain paths and variables need to be set. This section explains each variable in detail. Furthermore the env-template file is an example of such a file.
The REMOTE_PATH is set by the user individually and points to the directory on the HPC in which the user wants to create and run this project.
REMOTE_PATH=<Path>
The DATASET_NAME defines the name of the dataset and acts as the main tracker of results generated with scripts (Every result directory generated by a script or workflow is with a directory named after the DATASET_NAME variable). Only use letters and "_".
DATASET_NAME=<Name of Dataset>
RUN_NAME_IN and RUN_NAME_OUT are secondary tracker of results. The input and output is tracked accoring to this variables. The input and output directories in addition to the script or workflow are named after RUN_NAME_OUT. With the RUN_NAME_OUT variable the input to the script is defined.
RUN_NAME_IN=<Name>
RUN_NAME_OUT=<Name>
DATA_PATH_IN points to the raw data input of the current dataset. It is used only in the first processing scripts. Path has to end with "/"
DATA_PATH_IN=<Path>
Sepcific scripts need the type of flowcell and kit with which the dataset has been generated.
FLOWCELL=<Flowcell type>
KIT=<Kit type>
FILES_PER_SUBDIR defines the amount of files which are placed in each subdir in the script "basecalling_guppy_array.sh"
FILES_PER_SUBDIR=<Number of files>
For the local installation of the guppy basecaller a path needs to point to the "guppy_basecaller" command in order to use it.
GUPPY_BASECALLER_PATH=<Path to Installation>
For the local installation of the guppy demultiplexer a path needs to point to the "guppy_barcoder" command in order to use it.
GUPPY_DEMULTIPLEXING_PATH=<Path to Installation>
For the local installation of the qcat demultiplexer a path needs to point to the "qcat" command in order to use it.
QCAT_DEMULTIPLEXING_PATH=<Path to Installation>
The nanofilt filtering scripts need a quality score and a min, max length variable input
NANOFILT_QSCORE=<q score>
NANOFILT_MIN_LENGTH=<min length>
NANOFILT_MAX_LENGTH=<max length>
For the local installation of the kraken2 classifier a path needs to point to the "kraken2" command in order to use it. Furthermore a reference database needs to be specified.
PATH_KRAKEN2=<Path to Installation>
PATH_KRAKEN2_DB=<Path to Database>
For the local installation of the qcat demultiplexer a path needs to point to the "qcat" command in order to use it.
PATH_KRONATOOLS=<Path to Installation>