Kneaddata version 0.10.0
I would like to know if its possible using kneaddata to save the SAM files produced by bowite2? By default the code write sam file to dev/null/ I will be interested to keep the SAM files from the mapping to the human genome.
I tried by passing this argument: bowtie2-options " -S kneaddata_output/" or “-S ./”. But the log keep indicating -S /dev/null
Is it possible without editing the file bowtie2_discordant_pairs.py?
I thank you in advance for the help.