Auto-format sample names

[nick-youngblut]

Description of feature

The nf-core/rnaseq pipeline will generate a salmon.merged.gene_lengths.tsv file in which the sample names have been modified if the sample names contain a dash (- => .).

It would be helpful if the differentialabundance pipeline automatically did the same in order to prevent the DIFFERENTIALABUNDANCE:VALIDATOR process from failing.

[pinin4fjords]

Could you expand on this a little please? Is differentialabundance correcting the sample names in some files and not others, causing the validation to fail?

[nick-youngblut]

Is differentialabundance correcting the sample names in some files and not others, causing the validation to fail?

Yes, at least the same names in salmon.merged.gene_lengths.tsv are modified so that dashes are converted to dots ('-' => '.'). It would be helpful if the sample naming was standardized across all output (e.g., add a sample renaming process to the start of the pipeline).