Jonathan Oribello

## Description This file has been retired as the relevant columns are now generated on the fly where used by GeneLab visualization. ## Proposed Solution Remove generating code.

[BulkRNASeq] Update default publish output directory when processing GLDS data

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## Description Current default output directory is named after GLDS ID; however, with release of OSDR, the default directory should indicate both the OSDR and GLDS IDs by default. ##...

## Description Factor value strings can collapse into the same R safe strings. E.g. "p53+/Fbxw7+/-" and "p53-/Fbxw7-/-" Both collapse into "p53..Fbxw7..." This breaks DESeq2 R scripts. ## Steps to Reproduce...

## Description Certain datasets have experimental groups of single samples. This current breaks differential expression approaches and likely means differential expression will be impossible. ## Steps to Reproduce 1. Create...

Transfer from dev issue 149 - [ ] Annotation Reference Table Support

Planned Fixes (Marked as done when this PR includes implementations): - [x] #20 - [ ] #22 - [x] #32

## Expected Behavior Memory specified for STAR_ALIGN should be appropriate. ## Actual Behavior Memory specified is often insufficient when using larger references (i.e. from certain organisms like homo sapiens). Depending...

## Expected behavior Workflow launch using approach 3 (custom runsheet) should not require setting `gldsAccession` ## Actual behaviour Workflow checks if `gldsAccession` is unset and raises an error on attempting...

[BulkRNASeq] V&V program mistypes samplenames as ints when possible

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# Description When sample names can be interpreted as numerical instead of string (e.g. 12), certain V&V checks incorrectly do so result in failure to match '1' and 1. ##...