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Update rna-seq.nf

Merged Jonathan Gesell requested to merge 129-Fix_FastQ_Error into develop
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# v.2.x.x (indev)
**User Facing**
**Background**
* Corrected file search parameters due to name inconsistency (#129)
# v2.0.0
**User Facing**
* Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility)