Added optional parameter --nsubgenes

[jonoave]

Many thanks to contributing to qbic-pipelines!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

• This comment contains a description of changes (with reason)
  Added optional parameter --nsubgenes, due to potential errors with small dataset like miRNAs
  https://www.biostars.org/p/456209/

• If you've fixed a bug or added code that should be tested, add tests!

• Ensure the test suite passes (nextflow run . -profile test,docker).
  Tested with the following options, completed without errors:

nextflow run jonoave/rnadeseq -r add_feature_nsubgenes -profile test,cfc 
nextflow run jonoave/rnadeseq -r add_feature_nsubgenes -profile test,cfc --nsubgenes 500

• Documentation in docs is updated
  Not updated.
• CHANGELOG.md is updated
  Updated with line on v 1.4.1
• README.md is updated
  Not updated.

Learn more about contributing: https://github.com/qbic-pipelines/rnadeseq/tree/master/.github/CONTRIBUTING.md

[ggabernet]

Hi @jonoave , thanks a lot for the helpful contribution. I just have a comment regarding the parameter name, which could be a bit more precise. Other than that it looks good!

[d4straub]

I think the change that Gisela proposed needs to be also done in almost all other files (not in the R script though).

[jonoave]

I think the change that Gisela proposed needs to be also done in almost all other files (not in the R script though).

Thanks for the reminder Daniel, I've made the changes to the other files as well, and tested the rerun on cluster with
nextflow run jonoave/rnadeseq -r add_feature_nsubgenes_dev -profile test,cfc --vst_genes_number 500

The pipeline completed successfully

[ggabernet]

Hi @jonoave ,

thanks for the changes, looks good to me now, I just have a minor comment. The failing tests are due to some updates that are needed in the CI workflows, etc. That can be fixed in a separate PR so don't worry about them...

[ggabernet]

Great, thanks for your contribution @jonoave , once the tests pass we can merge!