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 script.


These are the default parameters set in the src/irfinder/ 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