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Versioning and Reproducibility

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Jill V. Hagey, PhD edited this page Aug 2, 2022 · 4 revisions

Version Control and Reproducibility

Version control is important for reproducibility of pipeline results.

Version Control

You can install a specific branch or tag of a pipeline using the -b argument for git clone:

git clone -b v1.0.0 https://github.com/CDCgov/phoenix

or you are using the nextflow run command then you can run a particular "revision" (aka version) of the pipeline to run it by passing either a git branch, tag or commit SHA number) with the -r argument like:

nextflow run cdcgov/phoenix -r v1.0.0 -profile <singularity/docker/custom> -entry PHOENIX --kraken2db $PATH_TO_DB

If you want to always run the latest version then pass the latest parameter:

nextflow run cdcgov/phoenix -latest -r v1.0.0 -profile <singularity/docker/custom> -entry PHOENIX --kraken2db $PATH_TO_DB

Updating PHoeNIx

If you are using nextflow run cdcgov/phoenix you might see this NOTE that your version is out of date:

N E X T F L O W  ~  version 21.10.6
Launching `cdcgov/phoenix` [confident_heisenberg] - revision: f467139cb7 [v1.0.0]
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [91d2ad9904]

To upgrade your version to the latest patch run nextflow pull cdcgov/phoenix and you will see something like this:

Checking cdcgov/phoenix ...
 Fast-forward - revision: 91d2ad9904 [v1.0.0]

Now you are all good to go!

What version am I running?

PHoeNIx always tells you what version it is in its initial output:

PHoeNIx_Version.PNG

DISCLAIMER: The identification methods used and the data summarized are for public health surveillance or investigational purposes only and must NOT be communicated to the patient, their care provider, or placed in the patient’s medical record. These results should NOT be used for diagnosis, treatment, or assessment of individual patient health or management.

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