Bugfixes pathway analysis

[SusiJo]

PR checklist

Fixes the ggsave error when many genes are DE.
With many genes being DE, one might need to adapt resource requirements.
Therefore, usage docs were updated to better document what to do in case of 137 error (OOM-out of memory).

  Quitting from lines 1936-2369 [load_PA_libs] (RNAseq_report.Rmd)
  Error:
  ! One or both dimensions exceed the maximum (50000px).
  - Use `options(ragg.max_dim = ...)` to change the max
    Warning: May cause the R session to crash
  Backtrace:
   1. ggplot2::ggsave(...)
   2. ggplot2 (local) dev(...)
   3. ggplot2 (local) png_dev(..., res = dpi, units = "in")
   4. ragg (local) f(...)
   5. ragg:::get_dims(width, height, units, res)
  Execution halted

Fixes the duplicate row.names error due to duplicate gene_names. Solved by concatenating Ensembl_ID_gene_name.

  Quitting from lines 2150-2607 [load_PA_libs] (RNAseq_report.Rmd)
  Error in `.rowNamesDF<-`:
  ! duplicate 'row.names' are not allowed
  Backtrace:
      ▆
   1. ├─base::`rownames<-`(`*tmp*`, value = mat$gene_name)
   2. └─base::`rownames<-`(`*tmp*`, value = mat$gene_name)
   3.   ├─base::`row.names<-`(`*tmp*`, value = value)
   4.   └─base::`row.names<-.data.frame`(`*tmp*`, value = value)
   5.     └─base::`.rowNamesDF<-`(x, value = value)
  Execution halted

Ensembl_ID_gene_name string can be split afterwards to filter out duplicates if desired.

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[famosab]

Linting fails probably because you need to update to the latest template :)

[famosab]

I am not so familiar with R but the changes seem to be fine just coding / guideline wise :)

[SusiJo]

Linting fails probably because you need to update to the latest template :)

Yes, that would solve the linting issue. However, we will move to the nf-core/differentialabundance pipeline soon which makes the template update obsolete. These changes are implemented to prepare a last release with some bugfixes.

[famosab]

🚀

[SusiJo]

@famosab thanks for reviewing!