Update Mnase-seq pipeline

[Bios-seG]

I noticed the Mnase-seq pipeline is deprecated.
I want to update it from DSL I to DSL II, which implies new modules and a refactoring of the main workflow.

The current pipeline is really huge, so maybe the refactoring could simplify it a bit, I was thinking of the following pipe :

1. Raw read QC (FastQC)
2. Adapter trimming (Trim Galore!)
3. Alignment
4. Mark duplicates
5. Merge alignments from multiple libraries of the same sample
6. Call nucleosome positions and generate smoothed, normalised coverage bigWig files that can be used to generate occupancy profile plots between samples across features of interest (DANPOS3)
7. Normalise the wig files in order to compare them
8. Generate gene-body meta-profile from normalized bigWig files

Let me know if you like the idea.

[mashehu]

please also post this on the slack channel: https://nfcore.slack.com/archives/CKT4FLYR5 maybe you can find somebody there to collaborate for this effort

[Rohit-Satyam]

Hi @mashehu. I would like to contribute to this pipeline. Which branch should I start working with?