---
tags: pipeline
---

# nf-core/differentialabundance

## Attendees
Jonathan Manning, Oskar Wacker, Gisela Gabernet, Alexander Peltzer

## General Discussion

* @JonathanManning created a module for differential expression analysis with DESeq2
* Uses template to side-step lack of module bin/ dir, which has side benefits in not requiring a CLI or associated libraries (optparse), allowing direct use of the DESeq2 biocontainer
* Separates plotting functionality. I think that makes the code more maintainable an allows for reuse by non-DESeq code in future (but others may disagree!). - Jon
* There is a qbic/rnadeseq pipeline from qbic which can serve as a starting point
* I'm not precious about the DESeq2 PR if it creates difficulties in porting existing pipeline. - Jon
* I do think modules should be generic though - i.e. make few assumptions about the upstream pipeline. - Jon

## Action points

* Oskar will go through PR from Jonathan
* Oskar will get the qbic pipeline to nf-core now
* Agreed on name:differentialabundance
* Gisela will add the slack channel etc pp

## Workflow concept

flowchart TD
    Module{Module} & fileORfolder[fileORfolder] & RobjectFile[[RobjectFile]] & param([param])

flowchart TD
    CountTable[CountTable.txt] --> Input_FeatureCounts{Input_FeatureCounts}
    StarRsemFolder[StarRsemFolder] --> Input_StarRsem{Input_StarRsem}
    StarSalmonFolder[StarSalmonFolder] --> Input_StarSalmon{Input_StarSalmon}
    Input_FeatureCounts & Input_StarRsem & Input_StarSalmon --- empty1(( )) --> StandardInput[StandardInput]
    design[design.txt] & StandardInput & meta[meta.tsv] --- empty2(( )) --> DESeq2{DESeq2}
    DESeq2 --- empty3(( )) --> sizeFactors[sizeFactors.tsv] & plotDispEst[plotDispEst.png/pdf/svg] &  RSummarizedExp1[[RSummarizedExp1]] & counts[counts]
    
    RSummarizedExp1 & rlog/vst/both([rlog/vst/both]) --- empty4(( ))
    empty4 --> Transform{Transform}
    empty4 -.-> Plots{Plots*}
    Transform --- empty5(( )) --> RSummarizedExp2[[RSummarizedExp2]] & normalizedCounts[normalizedCounts]
    RSummarizedExp2 --> BatchCorrect{BatchCorrect}
    BatchCorrect --> RSummarizedExp3[[RSummarizedExp3]]
    RSummarizedExp3 
    
    empty4 & contrastfile[contrastfile.txt] & logFCthreshold([logFCthreshold]) & pvalthreshold([pvalthreshold]) --- empty7(( )) --> Contrast{Contrast}
    Contrast --- empty8(( ))
    empty8 --> final_table[final_table.tsv] & DE_table_contrast[DE_table_contrast.tsv]
    
    RSummarizedExp3 & otherstuff[otherstuff] & report.rmd[report.rmd] --- empty9(( )) --> WriteReportMakePlots{WriteReportMakePlots}
    WriteReportMakePlots --- empty10(( )) --> report.html[report.html] & plots[plots]