- [x] section on data reuse.
- --> Make available cortex pf3k vcfs, comas assemblies, clockwork (cortex) 1017 (1000 + 17 Comas) vcfs --> Accessions for 700 pf3k BAMs
[x] container: install python env from requirements.txt. See martin's clockwork container setup for how to interact with repo on local filesystem. [x] container: RScript installing all dependencies in one go, called by singu def file. [x] container: add enaDataGet for downloading from ENA? [x] container: ensure can run scripts which rely on nesting_paper py package (installed in dev mode from analysis/scripts) [x] add Michael's singularity bind options + check singularity workdir
[x] Re-run all workflows [x] pf3k bams: script to download them