A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

How does creating "sub-modules" work when the're already a main module?
Right now there is a `rasusa` module, but some time ago rasusa added different subcommands: `reads` and `aln`, `reads` being the original functionality and `aln` the new one to filter BAM files. Normally, this would mean having `rasusa/reads` and `rasusa/aln`, but there already a module covering the "top level".
How to handle this correctly?

In the past we've gone with moving/renaming the original to duplicate the main command (e.g. kraken2_kraken2) or just make the new module with a different name including the version (AMPcombi -&gt; ampcombi2)

Do you know how many pipelines are already using rasusa?

Just bacass it seems: <https://github.com/nf-core/bacass/tree/2.6.0/modules/nf-core/rasusa|github.com/nf-core/bacass/…/rasusa>

Maybe you can ask if they are ok if you were to kill it and replace it

Probably deprecate the original one and replace with the new name