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TheJacksonLaboratory / cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines
MIT License
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Pre-release and/or compatibility with `nextflow pull/run` #1

Closed wflynny closed 2 years ago

wflynny commented 2 years ago

Hey CS team, this is a great resource!

Would it be possible to add a (pre-)release to the GitHub repo? Currently there's a tag 0.1.0 from a week ago and you just need to create a release from it (which could be automated in the future if needed).

This would allow compatibility with

nextflow pull -r 0.1.0 --workflow wgs ...
# and
nextflow run -r 0.1.0 --workflow wgs ...

I'd argue this is preferred over encouraging users to git clone the repo because (a) nextflow can assert the pipeline being run corresponds to a specific version (it can manage multiple versions of pipeline) (b) depending on when the repo was cloned, it may not be in a stable state or may be in a developmental state, and you have to rely on the end user to manage git pull/fetch

Cheers

MikeWLloyd commented 2 years ago

Thanks for this, I wasn’t aware of this functionality. I think this is something we can and should do.

I held off on making a release on GitHub as we mirror from bitbucket to GitHub and I wasn’t sure if the mirroring affects releases on git. I will experiment, and we can get something worked out.

wflynny commented 2 years ago

Perfect, works like a charm now. Thanks @MikeWLloyd!

> nextflow pull TheJacksonLaboratory/cs-nf-pipelines -r v0.1.0
Checking TheJacksonLaboratory/cs-nf-pipelines ...
 done - revision: c6aeda5ad0 [v0.1.0]
> nextflow info TheJacksonLaboratory/cs-nf-pipelines -d
 project name: TheJacksonLaboratory/cs-nf-pipelines
 repository  : https://github.com/TheJacksonLaboratory/cs-nf-pipelines
 local path  : /home/flynnb/.nextflow/assets/TheJacksonLaboratory/cs-nf-pipelines
 main script : main.nf
 revisions   :
   c6aeda5ad0 main
 * c6aeda5ad0 v0.1.0 [t]