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ncihtan / data-models

Schema.org Data Models for HTAN
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Errant fields in CDS Sequencing template #434

Open aclayton555 opened 3 months ago

aclayton555 commented 3 months ago

Two attributes (cDNA Length and cDNA Offset) that were accidentally included in this initial version of the template. These are optional attributes and can be ignored by users currently, but we should remove these in the future. Likely due to a clash or issue with the DAG, as commented in https://github.com/ncihtan/data-models/issues/396

aditigopalan commented 2 months ago

I think this was fixed here . Is there further work to be done on this?

aclayton555 commented 2 months ago

Cross check with https://github.com/ncihtan/data-models/issues/436

PozhidayevaDarya commented 2 months ago

Cross check with https://github.com/ncihtan/data-models/issues/436

To the best of my knowledge, I don't think this issue co-occurs wtih 436. When I check the configs for the cds genomics mapping scripts it does not contain anything referencing CITE-seq and generally, CITE-seq was only implemented very recently.

Since that issue + PR is separate I think they can be moved forward independently from this one. @adamjtaylor

aditigopalan commented 2 months ago

@PozhidayevaDarya @adamjtaylor I just generated a Multiplexed CITE-seq Level 1 manifest using dca staging and still see cDNA length and cDNA offset, is this still expected? I think I saw and fixed a similar issue in #417

Do we know where specifically these DAG loops are?

aclayton555 commented 2 months ago

24-7 close out: Okay if this rolls into 24-8 sprint.

aclayton555 commented 1 month ago

Check is these cDNA attributes are still appearing:

aditigopalan commented 1 month ago

Still seeing cDNA length and cDNA offset here, as optional fields. Is that expected?

aclayton555 commented 3 weeks ago

Check whether these are still in the CDS seq template. If they are, document this, and take no action, but be sure to communicate to contributors that they can ignore these two attributes.

Action: with every release, have latest blank templates auto-generated and push to a folder in GH @aclayton555 backlog a ticket for this. Doing this in MC2 - pull this over.

aclayton555 commented 3 weeks ago

Confirmed: these two attributes are still in the CDS seq template