Singularity container

Once we have the final workflow ready and running, we can start building a Singularity container. Details to be added soon.

• STAR, chromap, fastp, bcltools, R + Bioconductor / Seurat / ArchR
• use existing recipes for other projects and adapt

changed milestone to %Snakemake workflow specifics and Reproducibility

assigned to @carnold

changed the description

added Currently doing label

Container for command line tools is built and seems to work. Untested with a real analysis.

Current issuess:

• je-suite default memory (asked in EMBL chat)
• bcl-convert missing, not sure how to integrate it (asked in EMBL chat)

The R image is missing yet, will be build once I know which packages to install.

R container has been built, the extra packages from the last rule (RNA cell calling QC) is missing but in principal, it is done and can easily be adopted.

I re-created the containers, currently re-running an analysis to test. Snakefiles are adjusted accordingly

Containers seem to work, I successfully run all rules (except the yet unfinished kneeplot rule) with the containers. Al that is elft is uploading to the Zaugg singularity hub registry and linking it via a publicly accessible URL, currently the Singularity images are still hard-coded

All done. Images can be retrieved publicly now from the Zaugg container registry, I added the commands for this also in the Singularity README here in the Git

closed