Implementation of IsoformSwitchAnalyzeR

[jesseangelis]

Description of changes

In reference to issue #148

Dear rnasplice team, as my colleague discussed with you on slack on 15 February, I have added IsoformSwitchAnalyseR to the pipeline.

IsoformSwitchAnalyzeR is a powerful tool for identifying isoform switches in transcript data.

IsoformSwitchAnalyzeR takes a Salmon results directory as input. If it finds genes with isoform switches, it produces publication-quality plots visualising these switches. A separate set of switch plots is generated for each contrast if that contrast contains significant switches. Two .csv files are also created, a summary and the main data frame. The .rds of the main R-list is also returned.
This results in the following file structure:

isoformswitchanalyzer
|-- results
| |-- Condition1_vs_Condition2
| | |-- 01_switch_plot_gene1.pdf
| | |-- 02_switch_plot_gene2.pdf
| | |-- 03_switch_plot_gene3.pdf
| |
| |-- Condition2_vs_Condition3
| | |-- 01_switch_plot_gene4.pdf
| | |-- 02_switch_plot_gene5.pdf
| | |-- 03_switch_plot_gene6.pdf
|
|-- isoformswitchanalyzer_isoformfeatures.csv
|
|-- isoformswitchanalyzer_summary.csv
|
|-- switchlist.rds

Details

A new local module was added calling an R script in bin.
The module is called from the rnasplice workflow.
A new test for IsoformSwitchAnalyzeR was added.
Documentation, config scripts, etc. were updated according to the guidelines.

Some of the commits are from merges with the updated master branch.

The lint checks failed. But they also failed before I implemented the changes.

PR checklist

• This comment contains a description of changes (with reason).
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[jma1991]

Hi Jesse,

Thank you so much for submitting a pull request for IsoformSwitchAnalyzerR!

I’ve added myself along with two other maintainers to help review it.

@bensouthgate, if you’ve got a moment, could you take a look?
@lathikaa, could you or someone from the bioinformatics team also give it a review when possible?

Thanks again for your contribution!

Best regards,
James

[jma1991]

@lathikaa Can you also replicate the changes to the metro-map which Jesse has committed using the original Canva template?