Workflows for "Analysis" page

[nekrut]

Please add the following workflows:

Regulation

#workflow/github.com/iwc-workflows/ChIPseq_PE/main

Transcriptomic

#workflow/github.com/iwc-workflows/rnaseq-pe/main

[nekrut]

Merging in content from an archived issue:

---

• variant calling for haploid and diploid cases is done -> needs to be included to IWC. This is contingent on snpEff upgrade updated snpeff version, fixed gb parsing py script tools-iuc#6387
• ChIP-seq = @wm75
• transcriptomics = @pavanvidem

UPDATE 10/10/2024

• snpEff is done. Waiting for merge
• new ChIP-Seq WF that handles replicates and controls Add new ChIP-Seq WF that handles replicates and controls iwc#581 (Ready to review)
• Updated paired-end bulk RNA-seq with QC and featureCounts Update PE RNA-seq workflow iwc#544 (Ready to review)
• Updated single-end bulk RNA-seq with QC and featureCounts Update RNA-seq single-end workflow iwc#580 (Ready to review)
• New bulk differential expression analysis, filtering and plotting first release of RNAseq DE analysis, filtering and plotting workflow iwc#582 (Ready to review)
• Single-cell RNA-seq analysis preprocessing and clustering Add a new scRNA workflow for standard analysis using Scanpy iwc#556 (Ready to review)
• Downstream analysis of single-cell clustering Add files for pseudobulk workflow using decoupler and edgeR iwc#573 (Ready to review)
• A single-cell ATAC-seq workflow under development

UPDATE 10/31/2024

• https://dockstore.org/workflows/github.com/iwc-workflows/haploid-variant-calling-wgs-pe/main:main?tab=info

[hunterckx]

Resolved by #138