Roadmap v1.0.0

[sreichl]

Crucial tasks

• v3.0.0 scrnaseq_processing_seurat#26
• Enable continuity i.e., End-to-End execution #34
• Module usage in Projects - Wiki entry with full code, config, etc. #29
• Enable module usage directly from GitHub #41
• create Quick Start Guide #39
• create fetch_ngs module
  • iseq -i test.txt -g -t 10 -p 10
  • -a does not work
• v1.0.0 rnaseq_pipeline#1

Recipes
Make End-To-End Recipes including Vignettes as GitHub Wikis

• ATACseq Analysis Recipe
  • (w/ Corces et al data) https://github.com/epigen/MrBiomics/wiki/ATACseq-Analysis-Recipe
• RNAseq Analysis Recipe
  • (w/ Corces et al data) https://github.com/epigen/MrBiomics/wiki/RNAseq-Analysis-Recipe
• Integrative Analysis Recipe
  • https://github.com/epigen/MrBiomics/wiki/Integrative-Analysis-Recipe
• scRNA-seq Analysis Recipe #38
• scCRISPR-seq Analysis Recipe https://github.com/epigen/MrBiomics/wiki/scCRISPRseq-Analysis-Recipe

Misc

• add to all YAML environment specifications nodefaults #30
• test portability #28
• Provide example/test data and results for each module #20
• test instructions provided on Snakemake workflow catalogue using snakedeploy for my modules #7
• make all resource files input to rules #40

Docs

• add to docs "prerequisites" in terms of skills #32
• polish all config file documentations #31
• Logo, with RtH and RB
• Add to Resources on Bock Lab Website #33

Project Management

• lift tasks from my Notion to GitHub (here) #5
• work through master note in Notion #18

[sreichl]

• docs on config use:
  Now my recommendation is to NOT use any configs directly but always via params so its traceable. Sadly, my own modules do not adhere to it 100% yet as it was a later learning. Similar/related learning: if you use resources that are defined in configs they should be inputs to the rule not params.
  defining params for configs seems redundant but makes rules more readable/transparent and enables traceability for Snakemake.
  related: Bug accessing config variable from within the shell directive in a module snakemake/snakemake#1688