Enable module usage directly from GitHub

[sreichl]

Due to three unresolved Snakemake issues related to module usage from GitHub, we will access auxiliary source files using params instead of snakemake@source in R and remove global.yaml usage.
This implies that the full snakemake (not minimal) installation is required for the usage of MrBiomics and it's modules.

Unresolved Snakemake issues

• R sourcing: Error in rule with Rscript from imported module  snakemake/snakemake#2205
• Python sourcing: Relative import in python script not working when using a module from Gitlab snakemake/snakemake#1632
• global.env error: FileNotFoundError for global.yaml When Loading Module via github() snakemake/snakemake#3212

Tasks

• doc that full Snakemake is required. Minimal snakemake requires to uncomment global env BUT leads to loss of GitHub directive function when used as module. Additionally, when installing, document the shift away from the global environment to ensure the full SnakeMake is installed instead of the minimal version. Also, review the wiki and other documents to update any mentions of global environment variables. This is likely found in the sustainability and reproducibility section.
• comment global.yaml
  • https://github.com/epigen/enrichment_analysis
  • https://github.com/epigen/dea_limma
  • https://github.com/epigen/scrnaseq_processing_seurat
  • https://github.com/epigen/dea_seurat
  • https://github.com/epigen/mixscape_seurat
  • https://github.com/epigen/atacseq_pipeline
  • https://github.com/epigen/genome_tracks
  • https://github.com/epigen/unsupervised_analysis
  • https://github.com/epigen/spilterlize_integrate
• replace snakemake@source with params solution
  • https://github.com/epigen/enrichment_analysis
  • https://github.com/epigen/dea_limma
  • https://github.com/epigen/scrnaseq_processing_seurat
  • https://github.com/epigen/dea_seurat
  • https://github.com/epigen/mixscape_seurat