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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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pigx_bsseq for RRBS #145

Closed xie186 closed 4 years ago

xie186 commented 5 years ago

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 add

......
    RRBS: --rrbs  ## OR empty

then in the snakemake file, we can add config["general"]["RRBS"] in trim_galore command line.

alexg9010 commented 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