Closed xie186 closed 4 years ago
Hi @Xie186,
Sorry for the very late reply.
If you want to pass arguments to trim galore you may do so in the tools section of the settings file, where each tool we use has an 'args' parameter that is forwarded to the tool call.
Hope this helps, Best Alex
Hi, thanks for develop pigx_bsseq. I'm wondering whether it is possible to allow us to enable
--rrbs
(https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md#rrbs-specific-options-mspi-digested-material) so that pigx can process MspI digested RRBS data. Thanks in advance.For example, in the
general
section, if we addthen in the snakemake file, we can add
config["general"]["RRBS"]
intrim_galore
command line.