Run TC hunter

Run TC_hunter.nf

Before running, make sure you have a config file with all required information (see Config).

$ nextflow TC_hunter.nf -c <file.config> [-with-report <report name>]

Run TC_hunter_BWA.nf

Before running, make sure you have a config file with all required information (see Config).

$ nextflow TC_hunter_BWA.nf -c <file.config> [-with-report <report name>]

Run IGV separately

In order to get the IGV figures you need to have GUI available. If not; you can run IGV separately when TC-hunter is finished. Run one .bat file for each sample.

$ igv.sh -b <sample_name.bat>