TODO

# Todo

* [ ] Documentation
  * [ ] Installation (Snakemake)
  * [ ] Using config files
  * [ ] Description of all modules

* [ ] Tests
  * [ ] Create dataset with observations for the following cases:
    * [ ] Deletion
    * [ ] Insertions
    * [ ] BND
    * [ ] SNVs, Indels, hom and het
    * [ ] CNV ~ 50kB
    * [ ] Ref set for CNV
    * [ ] Repeat Expansion
    * [ ] Genome Ref
  * [ ] Snakemake test cases
  * [ ] Automate with GitHub

* [ ] New Modules
  * [ ] Modification analysis with https://github.com/EmanueleRaineri/cvlr
  
* [ ] Docker
  * [ ] Create dockerfile
  * [ ] Automate with GitHub/DockerHub
  * [ ] Integrate dependencies? Docker-Margin-Deepvariant?

* [ ] Circos overview plot
  * [ ] CuteSV/Sniffles BND tracks
  * [ ] CNVkit depth track
  * [ ] CNVkit copy number
  * [ ] SNV, Indel density?
  * [ ] Loss of Heterozyosity, look in MegSAP for other Tracks
  * [ ] Repeat Expansions highlight, with label?

* [ ] Integration to GSVar
  * [ ] Either extend supported filenames in GSVAR or change filenames generated by megLR
  * [ ] Annotate variants! Either with in House database, which needs to generated or with OMIM/External data

* [ ] Check and maybe reanalyze old projects
  * [ ] 20110Ia001 ? Phasing was done

* [ ] Compare reference genomes:
  * [ ] GRCh38_alt_decoy
  * [ ] GRCh38_core_only
  * [ ] T2T_CHM13

* [ ] Change hardlinked executables to conda:
  * [X] MultiQC
  * [X] Stringtie
  * [ ] Minibar
  * [ ] Sqanti

* [ ] Make pipeline less IMGAG specific
  * [ ] Include CNVkit reference, change ref creation
  * [ ] Remove all links to external folders
  * [ ] Package all in Docker
  * [ ] Remove old and/or broken pathways

* [ ] Mamba support for environment creation
* [ ] Update tool versions (when tests exist)

* [ ] Amplicon (Dual Demux)
  * [ ] Demuxed samples should be located on top level
  * [ ] Change Variant Calling to Pepper_Margin_DV

* [ ] Error Messages:
  * [ ] No target region given for CNVKit
  * [ ] No ref given for CNVKit