rna-seq-workflow should copy all annotations

Question

rna-seq-workflow should copy all annotations

allaway opened this issue 5 years ago · comments

Robert Allaway commented 5 years ago

With the exception of ones that it is changing or making irrelevant, like "fileFormat" = .sf and "readPair"

Sara JC Gosline · Answer 1 · Mon Apr 15 2019 00:38:40 GMT+0800 (China Standard Time)

So there's an option to do this by the second clinical query, are there specific annotations we should add?

Robert Allaway · Answer 2 · Mon Apr 15 2019 09:23:12 GMT+0800 (China Standard Time)

Sorry, I don't understand. I am suggesting we copy all annotations over from fastqs processed with this pipeline to the output quant.sf files that are returned to Synapse.

Sara JC Gosline · Answer 3 · Tue Apr 16 2019 03:26:58 GMT+0800 (China Standard Time)

So we essentially do that already by the sample_query parameter - any annotations you want to pass along you put into this query, and it will ensure they are applied to the uploaded folder. I'm afraid of trying to do this automatically.

Robert Allaway · Answer 4 · Tue Apr 16 2019 04:34:30 GMT+0800 (China Standard Time)

Oh, interesting, that makes a lot more sense. I was missing a bunch of annotations on the NF2 quant.sf files, and I wasn't sure why.

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On Mon, Apr 15, 2019 at 1:26 PM Sara JC Gosline ***@***.***> wrote: So we essentially do that already by the sample_query parameter - any annotations you want to pass along you put into this query, and it will ensure they are applied to the uploaded folder. I'm afraid of trying to do this automatically. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATdmyOrQ3Alwpjp0By37hs2YInIyDWUrks5vhNKCgaJpZM4cso4g> .