Jonathan Oribello

Implementation Steps - [ ] Runsheet generation now ingests optional technical replicate group table - [ ] DESeq2 script updated to use tech. rep group data for four handling approaches

Additional considerations: - How to handle technical replicates on multiple levels (e.g. multiple tissue cuts and multiple library preps for same biological sample) - Group statistic and sample count -...

Potential route using within trim_galore adaptor auto-detection: https://github.com/FelixKrueger/TrimGalore/blob/0.6.7/Docs/Trim_Galore_User_Guide.md#adapter-auto-detection

I'll try using auto-detect by omitting the flag, will of course validate if the auto detect is consistent with direct user supply of the parameter.

Testing Results using GLDS-426_Truncated (Known to have Nextera adapters): ## CURRENT (With --illumina) ``` Input filename: EU236_R2_raw.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.7 Cutadapt version: 3.7 Number of cores...

- [x] Implemented in 3b7e0bab4017e90481359c48f9cf7c8837ed54d2 - [x] DPPD Updated in 2a56552