Improve documentation: Troubleshooting

[SusiJo]

Description of feature

Suggestion: Please add a troubleshooting section with common error messages that helps users to quickly understand what they're missing to get the pipeline running.

I suggest to make a collection of frequently occurring errors here where users can post their error messages and the solutions they have found.

[SusiJo]

Error message when using input_type salmon:

Exiting.
  Error: DESeq2.R could not find all of the specified quant.sf files!
  In addition: Warning message:
  In .local(x, row.names, optional, ...) : Arguments in '...' ignored
  Execution halted

--> Solution: Check for typos in your samplesheet.tsv and make sure the QBiC Codes match the folder names of the rnaseq output. In case of using a salmon_merged_gene_counts.tsv, the names of the samples should be also carefully checked, as they can follow a different naming convention than the salmon folders.
Example: salmon folder name: QXXXXX:_XXX-XX vs column name in salmon_merged_gene_counts.tsv QXXXXX_XXX.XX

[SusiJo]

Error in deseq.R -r 2.0

Error in assay(if (opt$rlog) rld else vsd) <- limma::removeBatchEffect(assay(if (opt$rlog) rld else vsd),  : 
   could not find function "if<-"
 Execution halted

[SusiJo]

Error when running pathway_analysis.R -r 2.0.1

Error in check.length("fill") : 
    'gpar' element 'fill' must not be length 0
  Calls: pheatmap ... rectGrob -> grob -> gpar -> validGP -> check.length

[WackerO]

Error in deseq.R -r 2.0

Error in assay(if (opt$rlog) rld else vsd) <- limma::removeBatchEffect(assay(if (opt$rlog) rld else vsd),  : 
   could not find function "if<-"
 Execution halted

This is fixed on dev