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biocompute-objects / GW-SMHS-BIOC6223

Repository for BIOC-6223 Bioinformatics graduate students midterm project
BSD 3-Clause "New" or "Revised" License
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Description domain: incorrect step names #117

Open jpat1546 opened 5 years ago

jpat1546 commented 5 years ago

If you were assigned this issue, the following feedback is relevant for your draft BCO.

Feedback

The name field is referring to the tool name- it looks like you guys have provided the description instead of the name. Please modify all step names. Refer to Description domain section of BCO Specification document for help. (Below I've provided 1 example from each of your BCOs; keep in mind this may not be the only line you have to modify)

@tkanholm https://github.com/biocompute-objects/GW-SMHS-BIOC6223/blob/bd41089b6cfe4136c4974d21a794c32720252b51/Student_BCOs/Tomas_Kanholm_BCO_000514.json#L40

@javidgmh https://github.com/biocompute-objects/GW-SMHS-BIOC6223/blob/b8bd696cf1f2efc2bca1d61cf2fcd00f5006d7f8/Student_BCOs/JavidGhaemmaghami_BCO_000533.txt#L40

@CanyuanYang https://github.com/biocompute-objects/GW-SMHS-BIOC6223/blob/b8bd696cf1f2efc2bca1d61cf2fcd00f5006d7f8/Student_BCOs/BCO%20of%20%22RNA-Seq%20Analysis%20of%20Differential%20Splice%20Junction%20Usage%20and%20Intron%20Retentions%20by%20DEXSeq%22-Canyuan%20Yang.json#L35

This issue has been placed as a card in the "To Do" column of your individual projects. Please modify and save your BCO on the BCO Editor, with the above feedback provided. Once you've made the modification requested in this issue, move the card to the "Done" column of your projects. Then address the other issues in your "To do" column.

Once all issues assigned to you are addressed (all modifications have been made), and your BCO is saved in the BCO editor, please refer to the instructions in #104.

Additional Resources

Please make the necessary modifications prior to 10/16. Comment below if you have any questions. Thank you.

tkanholm commented 5 years ago

Hi Janisha,

My BCO is for an integrated pipeline with a GUI. (called iMIR) My sense is that it was designed for ease of use and so, although it runs specific tools "under the hood", the steps themselves are built into the GUI. I put "remove adapter" as the step name because it is the name of the button you click to run the step, and put the version as 1.0.0, the version number for iMIR as a whole. I put the program(s) that each step runs, in this case CutAdapt, as a software prerequisite in the execution domain.

Is this the right way to go about this?

kee007ney commented 5 years ago

Great question. BCOs for the fully integrated packages tend to need more customization. Let's take a look in or after class, but it sounds to me like you've handled it very well and that this would enable someone to understand what was done. Version 1.0.0 of the software as a whole is expected to have a specific version of code for that button, so that would be appropriate. The only thing I'd suggest is to include a note to that effect in the Usability Domain.