Additional downstream processes written in DSL1 -- UPGRADE now to DSL2

[Jani-94]

Description of feature

Already forked from methylseq (written in DSL1) and added the following:

1. additional methylation calling with cgmaptools and general statistics (plots and tables) using cgmaptools.
2. coverage stats and other things using methylkit.
3. Create a plot of methylation levels across the TSS using viewBS.
4. Input a bam file and continue from there with methylation calling etc.

Will start to update code from DSL1 to DSL2.

Cloned & modified Github: https://github.com/FAANG/GSM-pipeline

[ewels]

Excited to see some of these improvements! I would definitely split them up rather than trying to tackle all at once. As such, it might be worth making a new issue for each.

For each addition, you'll need to:

• Check that the software is packaged in bioconda (and add it if not)
• Add a new DSL2 module to nf-core/modules (see tutorial and docs)
• Once that's approved and merged, open a pull-request against the dev branch of this repository to add the new module
  • Run nf-core modules install [your-new-tool]
  • Add the import statement and wire up the channels

I'd recommend starting with the simplest, once you've gone through the process once or twice it starts getting a lot easier..

Shout on Slack if you need any help with any of this!

[sateeshperi]

hey @Jani-94 are there any updates for what you proposed here ?