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

nf-core

Yes, I would strongly encourage you to contribute it to nf-core/modules

```INFO     Linting pipeline: '.'                                                                                                                                                                         
INFO     Linting module: 'nextdenovo'                                                                                                                                                                  
CRITICAL list index out of range ```

I am having this error with no more details.

Probably should ask in <#CE5LG7WMB|> about that

Hello, the nextdenovo module is under review, can I start working on integrating to the pipeline locally just to test how would it work or you prefer that I wait for it to pass the review?

Sure, you will just have to swap it out once it is in nf-core

but if your local module is similar / identical to the one in nf-core i dont think you have to wait; if you want it to actually get reviewed, I would recommend asking in <#CQY2U5QU9|>

For integrating it into genomeassembler I guess you can kind of follow how it is done for the other assemblers: e.g. here <https://github.com/nf-core/genomeassembler/blob/dev/subworkflows/local/assemble/main.nf#L47>

I have a mid-term plan to switch from `params.assembler`  to something that is more `meta.assembler` to be able to mix assemblers within one samplesheet (e.g. for comparing assemblers) but this is currently just an idea and if you follow the current approach of using `params.assembler` that would be great and once I migrate to some different strategy I will take care of switching it over

I would also ask you to do the housekeeping surrounding this, e.g. updating `CITATIONS.md`

And also the relevant files in `docs` : `output.md`  and `usage.md`  I am not sure if it is easily possible to stuff another assembler into the pipeline map, that might need to be reworked (by me) more generally.

I will follow the current approach and try to use other assemblers as reference.  I will change those files too. Thank you very much!