#feature : improvements - but that are not critical for now #2
Description
Minor buggs and enhancements to implement in the pipeline
- tutorial - wiki modification - instructions on how to use the quotes to pass arguments to R for filtering of taxa
- change "coverage" track to compass (assembly comparison - and direction)
- Compass track: improve modularisation for the little modules that are running on their own.
- find way to simplify the modules that are nearly similar - using same module but with different input and output eg. BWAMEM, SAMTOOLS ...
- Compass track: options to turn on/off submodules - eg when adjustements or rerun compass - the filtering process is only needed the first time - so make sure aslo that input are not dependents to each other
- quarto R script for filtering contigs - would have liked to keep xlsx for export BUT needed to switch to csv due to java problems
- same for Busco summary.qmd
- ind a better way to pass this filter expression to quarto - ? nexflow ${param} instead of what is now ? with special quotes ?