covid-19: Create "Assign to workflow step, workflow"

[boulund]

We will need a workflow that allows to assign specific samples to a certain workflow step (any workflow), in order to handle the backlog of SmiNet reporting.

The current plan:

• Create a workflow like "Create samples", that takes a list of samples and the name of the workflow+step that they samples should be assigned to

[chichackles]

File
https://github.com/Molmed/clarity-ext/blob/27230fe56cba4ec7169cf67686df167968714910/clarity_ext/data_cli.py
can do this from command line. The command is installed and available in the clarity-ext conda environment under the name clarity-data.

Usage:

First, activate the clarity-ext conda environment:

root@lims# su - glsai
glsai@lims$ source /opt/clarity/miniconda3/bin/activate clarity-ext

Then, the clarity-data command is available:

clarity-data --to-file move-artifacts-plan lims-id-1 lims-id2 [lims-idN...] 'SomeWorkflow' 'SomeStep' > 1.yml

review the file, then execute:

clarity-data --to-file move-artifacts --commit 1.yml

edited by Fredrik: cleaned up the formatting a bit

[boulund]

@chichackles , did you leave this comment here for your own future reference with regards to this issue, or is this intended as instructions on how to use it?

If the intention is to present usage instructions, I think it should be expanded a bit. We need to know which system user this needs to run as (I'm guessing glsai?), and if it has to run in a specific directory (I guess not?). There is also no information about the environment it requires (conda, or other dependencies). I'm guessing it expects the clarity-ext conda env, but I think we should document where that is located and how to activate it. Perhaps some examples of input files could be useful as well.

Are you still working on creating a GUI workflow+step for this as we discussed yesterday?

[chichackles]

Yes, I have put it here for reference. I would like to have everything in one place.
I hope to make it through GUI.

[boulund]

For the case of the large SmiNet backlog as of 2020-06-02, we moved all the affected samples manually using the clarity-data tool. Documentation in /opt/gls/clarity/users/glsai/sminet_backlog_20200602 on prod.

It would still be fantastic to have a workflow like this in Clarity, for the future.