Js current

[jscaber]

Significant changes to multiple pipelines.

Splicing pipeline

• Changed IRFinder to Singularity v2.0.0. Conda no longer supported
• IRFinder diff expression now using IRFinder Diff
• IRFinder now accepts same sorted BAM as all other tools - removed fastq support
• removed need for all python 2 environments

RNASeq DiffExp pipeline

• GO analysis now done for all, upregulated and downregulated genes
• PCA analysis no longer throws error if <8 PCs
• removed 'unlimited' memory which is not allowed on all clusters

Custom R venn script (not currently pipelined but useful)

• allows for Lfc threshold

Mapping pipeline

• BWA2-MEM now hardcoded, no longer supports bwamem
• Correct implementation of STAR2PASS Method

Pipeline Genesets

• Regexes fixed to remove hardcoding of ensembl.dir/geneset_all.gtf.gz and allow correct pickup

[jscaber]

I will merge this. I am the major user of most of those changes, but please be aware that bwa-mem in mapping.py now requires bwa-mem2.

[Acribbs]

Sounds good!