nf-core/riboseq - Module Plan - Githubissues

Caroline-99 / riboseq_pipeline

riboseq pipeline using nf-core tools and the features of Nextflow DSL2

MIT License

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nf-core/riboseq - Module Plan #1

Open JackCurragh opened 9 months ago

JackCurragh commented 9 months ago

Description of feature

Here I attempt to break down the required/desired modules for each processing stage of the workflow:

Pre-Processing

[X] Quality Control (FastQC)
[X] Cutadapt (Adapter Removal)
[ ] FASTP (Adapter Removal)
[X] UMI-tools (UMI handling)
[ ] Bowtie 1 (rRNA removal)
[X] HISAT2 (rRNA removal)
[ ] RiboDetector
[ ] SortMeRNA

Alignment

[ ] STAR (Genome Alignment)
[X] HISAT2 (Genome Alignment)
[ ] Bowtie (Transcriptome Alignment)
[X] Samtools (Alignment processing)
[X] BEDtools (Alignment processing)

Translated ORF Detection

[ ] RiboCode
[ ] RiboTaper
[ ] Ribo-TISH
[ ] Ribotricer
[ ] ORFik

Quantification

[ ] Salmon (Pusedoalignment + Quantification)
[X] featurecoutns (Quantification)
[ ] RiboCode/ORFcount

Differential Expression

[ ] Riborex (DE) (DEseq2, EdgeR, Voom)
[ ] Anota2Seq (DE)
[ ] DeltaTE (DE)

Please reply here with any other packages we should consider!

Caroline-99 commented 9 months ago

Yeah I think the module plan is very good, thank you for doing it. We could also integrate subsampling at the start of the pipeline. Ed had proposed this for my dissertation, but I couldn't do it it due to time constraints. I have now added FASTP to our pipeline and am in the process of implementing subworkflows. Once I get it working, I will update everything on github.