IRFinder can use both fastq and bam files. To use bamfiles please set the parameter $use_bam_input_files=1, and =0 to use fastq files in the as_config.sh script.
These are the default parameters set in the src/irfinder/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the IRFinder manual.
Base folder of the index files.-r $indexdir
Output directory. The output will be separated into case and control folder based on the basefolder of the according fastq file.-d $outdir
After all other options call space separated list of file paths to reads in fastq format. One pair of fastq files for paired-end reads.*yourFastqFile1_*1.fastq *yourFastqFile1_*2.fastq