Tidy up, Python and Docker fixes

bzhanglab / COSMO

COSMO: COrrection of Sample Mislabeling by Omics

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Closed drpatelh closed 1 year ago

drpatelh commented 1 year ago

Replaces changes in https://github.com/bzhanglab/COSMO/pull/6
Added minimal Dockerfile that can be used to build an image suitable for the docker tasks
Change to use the python script bundled in this repository rather than the Docker image for the method 2 process
Make --outdir a mandatory parameter and null by default for Cloud platform support
Some syntax and docs tidying up

cc @toddcreasy

zhiaos commented 1 year ago

thanks for the contributions.

drpatelh commented 1 year ago

Thank you for reviewing and merging! 🚀

drpatelh commented 1 year ago

Can confirm the pipeline is working on AWS Batch after merging in these changes

We will do further tests to ensure it is working with Singularity on a HPC too and contribute back if required.