[FEATURE REQUEST] Allow user configuration of Arioc's "<A>" element

LieberInstitute / BiocMAP

Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow

http://research.libd.org/BiocMAP/

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[FEATURE REQUEST] Allow user configuration of Arioc's "<A>" element #30

Open Nick-Eagles opened 1 year ago

Nick-Eagles commented 1 year ago

Currently, configuration of Arioc's "\<A>" element is inflexible, with specific settings hardcoded here and here. Add variables in the configuration files to support user-provided settings. This is particularly motivated by the new xmBQS option, which can have a significant effect on methylation-context calls for some data.

Nick-Eagles commented 1 year ago

Also, the version of Arioc will have to be updated to use >= 1.5, where the xmBQS exists.