Config File

The config file is a convenient way to hold all of the parameters for running the SPARCS pipeline. These parameters are automaticly filled in when running the sparcs command, but you can also edit the config file directly. The config file is located at workflow/config.yaml inside of the SPARCS output directory.

Config Parameter	Description
working_directory	Directory where all the output files will be written
vcf_file	Absolute path to the VCF file
gtf_file	Absolute path to the GTF/GFF file
ref_genome	Absolute path to the reference genome in FASTA format
name	Name for file prefixes
output_name	Name of the output directory
flank_len	Number of nucleotides on either side of the SNP for riboSNitch prediction
chunks	Number of chunks to split the VCF file into for parallel processing
temperature	Temperature for prediction of RNA secondary structure (in degrees Celsius)
ribosnitch_prediction_tool	Tool to use for riboSNitch prediction. Options are SNPfold and RipRap
structure_prediction_tool	Tool to use for RNA secondary structure prediction. Options are RNAfold and RNAstructure
riprap_min_window	Minimum window size for RipRap