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qiime2 / Keemei

Validate tabular bioinformatics file formats in Google Sheets
https://keemei.qiime2.org
BSD 3-Clause "New" or "Revised" License
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support validating Qiita formats #68

Closed jairideout closed 6 years ago

jairideout commented 8 years ago

Formats described here.

colinbrislawn commented 8 years ago

👍 Yes please. Qiita is pretty specific, so this would be a great.

jairideout commented 8 years ago

Keemei has experimental support for validating Qiita sample template files, it'd be great if you could try it out and let us know if anything isn't working for you!

colinbrislawn commented 8 years ago

Will do! I've got two projects (one super fresh, one legacy) that I can use for testing.

jairideout commented 8 years ago

Awesome, thanks!

colinbrislawn commented 8 years ago

As discussed over here, the standard term should now be 'Sample Information File', instead of 'Sample Template'

This is part of a larger issue: Qiita explicitly separates 'Sample Info' and 'Prep Info' into separate files without redundant content. As such, Keemei should probably validate 'Sample Info' and 'Prep Info' separately. Just to drive that point home, you could have 'Sample Info' throw errors when they include things like 'LinkerPrimerSequence' which are not 'Sample Info' and should instead be part of the 'Prep Info File'.

Let me know what you think. I understand that Qiita development is an ongoing process, so this may take time to address. Guidance from @antgonza would be helpful here.

antgonza commented 8 years ago

I think validating both (sample/prep information files) is important but also having a "nice" converter between QIIME/Qiita map files will be desirable. Thanks!

colinbrislawn commented 8 years ago

The converter would be an elegant way to help qiime people start using qiita. Simple validation would be a very good place to start.

And I'm super interested in testing these. Keep in touch!

jairideout commented 8 years ago

Thanks @colinbrislawn for letting me know of the new format name ("Sample Information File"). I wasn't aware of this change and will update Keemei's docs to use the new name and format spec URL.

@antgonza, is this page describing template files now obsolete? The link still works so it might be nice to redirect users to the new "info files" page.

This is part of a larger issue: Qiita explicitly separates 'Sample Info' and 'Prep Info' into separate files without redundant content. As such, Keemei should probably validate 'Sample Info' and 'Prep Info' separately.

Yep, Keemei will validate sample and prep info files separately because they are two different file formats. Right now Keemei only supports validating sample info files but there will be an option to validate prep info files in the future.

but also having a "nice" converter between QIIME/Qiita map files will be desirable.

Converting between file formats is outside the scope of Keemei but agree it would be nice to have an easy-to-use converter somewhere. I could see this converter living in Qiita, QIIME, or a standalone package/project.

Thanks for testing this out @colinbrislawn and for your input @antgonza! Let me know if there are other improvements I can make on Keemei's end.

antgonza commented 8 years ago

That link is still valid and it should always be up to date.

jairideout commented 8 years ago

Then what is the difference between a sample info file and sample template file?

antgonza commented 8 years ago

Just the name. As @colinbrislawn mentioned, discussed here: https://github.com/biocore/qiita/issues/1813

jairideout commented 8 years ago

Thanks, I've read through biocore/qiita#1813. Why does the sample template page still exist? I thought the template files were phased out in favor of information files?

colinbrislawn commented 8 years ago

There are 'sample info files' (biological metadata) and 'prep info files' (sequencing info). The term 'info' or 'information' replaces the old term 'template' in our public facing interfaces and documentation.

Where is the 'sample template' page? I'll get rid of it ;-)

Edit: 'Template' is used on these 3 documentation pages and all over the website.

jairideout commented 8 years ago

@colinbrislawn here's the "template" page:

https://qiita.ucsd.edu/static/doc/html/tutorials/prepare-templates.html

Maybe a redirect is more appropriate?

colinbrislawn commented 8 years ago

Woh, that's not listed in the menus anymore, and has indeed been fully superseded by https://qiita.ucsd.edu/static/doc/html/tutorials/prepare-information-files.html

I'll make that redirect...

jairideout commented 8 years ago

Okay, thanks!

colinbrislawn commented 8 years ago

This PR will should overwrite the existing page and will go live on the website over the weekend.

jairideout commented 8 years ago

Awesome, thanks @colinbrislawn!

jairideout commented 6 years ago

The next Keemei release (scheduled for sometime on or before Feb 15, 2018) has the updated Qiita file format name (sample information file instead of sample template file). Qiita file format support is also noted on the Keemei website. I think this issue is safe to close.