Design of Single Cell Pipeline

scMaestro is a workflow wrapper of a set of snakemake workflows. The snakemake workflow component SF_sc-smk-wl is used as a submodule of the repo for workflow wrapper. With the snakemake workflow as a seperate github repo, the wrappers we designed for internal use (SF_scMaestro)(private repo) and external use (scMaetro) can share the same snakemake workflow. This separation allows us to open-source our Snakemake workflow together with the wrapper for external users.

One feature of scMaestro is that the snakemake workflow will be copied to the analysis folder. The benefit that this provides a self-contained and reproducible environment for the analysis.

Another feature is that cMaestro relies on singularity. Singularity images will be created at the beginning of snakemake workflow run. This feature again improves the reproducibility of the analysis.

The singularity-related arguments use-singularity and singularity-args for snakemake workflow can be found here.