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

nf-core

Hello, running _test_ profile produces this error: any idea?

``` Genome 'GRCh37' not found in any config files provided to the pipeline.
  Currently, the available genome keys are:
  hg38, hg19```

this is weird since igenomes has "GRCh37" files. and igenome profile is being read by the pipeline

found the problem:
```igenomes_ignore = true```
has to be _false_

btw, I guess the need to turn off igenomes is because the profile needs to use custom fasta files. Yet, genome parameter is also being used with VEP which cannot be closed. I think the best solution to this to make another genome parameter for VEP.

yeah I think it's disabled by default because it's not used, we do plan to try and fix it

I also saw that CI tests are only running with -stub. Is this on purpose?

Unfortunately yes, I think that's part of our plans

<https://github.com/nf-core/raredisease/issues/663>

okay :smile: I am working on this pipeline to make skip_alignment possible :smile: lets see how it goes.