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SamStudio8 / reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
MIT License
68 stars 5 forks source link

Helper commands to initialise a pipeline #9

Open SamStudio8 opened 4 years ago

SamStudio8 commented 4 years ago

I'm torn on this as currently it's just a case of modifying some text files which is pretty straightforward. However, it would perhaps make sense for the config to be placed somewhere that could be read by any retic pipeline on any machine and it would be useful to not need to git clone the pipeline too.

SamStudio8 commented 4 years ago

I'm setting this as a future idea because although it makes sense to implement something that makes the pipeline easier to start up and kick off, it will cause trouble when versioning comes into play. What happens when I modify a rule, do we offer the option to init a new version pipeline, or an old version pipeline?

We could version control the Snakemake file and have a helper command download different versions? But what about the environment? Users will need the right versions of snakemake-minimal and the installed tools?