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LieberInstitute / SPEAQeasy

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
http://lieberinstitute.github.io/SPEAQeasy
MIT License
6 stars 4 forks source link

Make README informative and concise #28

Closed Nick-Eagles closed 3 years ago

Nick-Eagles commented 5 years ago

Most notably, information about docker setup is scattered throughout the README, often redundant, and the container versions are outdated. Other adjustments will be made in response to new users of the pipeline.

Nick-Eagles commented 4 years ago

The workflow.png diagram is also now outdated, as workflow structure has changed along with changes to inferring strandness, handling annotation, etc.

Nick-Eagles commented 4 years ago

@lcolladotor I was unsure how to handle the "Version Description" section at the bottom of the README. Specifically, we have not been updating GitHub version/release for SPEAQeasy since the work from Winter Genomics: is this something we should start doing and include in the README, or should this section be removed? Also, is the list of tested operating systems still appropriate for the README, or should it be moved to the docs (or removed)?

lcolladotor commented 4 years ago

I guess that the actual commit (the SHA id) is the "version number" for SPEAQeasy right now. So you can remove the version number that the WG team was using.

GitHub allows having "releases", so we could do that too at some point. Actually, I see that that's exactly what the WG team had been using at https://github.com/LieberInstitute/SPEAQeasy/releases. So hm... maybe we can bump it to 1.0.0 whenever we are ready for the pre-print release.

Anyway, is there a way to include the GitHub SHA on the log files created by Nextflow? That would be useful for debugging whenever a user asks a question. Maybe using https://stackoverflow.com/questions/1161869/how-to-get-sha-of-the-latest-commit-from-remote-git-repository.

As for the OS section, you can remove that now.

Nick-Eagles commented 4 years ago

For now, I've added the commit SHA in the main output from nextflow as you suggested (this commit)