Project management
See zenhub project management across this and related repos.
Pipeline project overview
Here is a high-level slide deck
See the wiki for full setup and execution instructions.
What is here
MetaPhlan3 + HUMAnN3 + StrainPhlAn + sratoolkit Docker+Singularity images
| DockerHub | SingularityHub |
|---|---|
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(see docker directory for Dockerfile and link to Dockerhub). - Instructions to run are kept in a wiki. - There is still work to be done turning bash scripts into a Python package with improved documentation, arguments, and versioning.
sratoolkit-only Docker+Singularity images
| DockerHub | SingularityHub |
|---|---|
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(see docker directory, but this is also included in the above all-in-one image.
a PyPi project for the curatedmetagenomics pipeline
See the python_pipeline directory
