Uploading Pair Metadata doesn't create links to case and control samples
Uploading metadata for a pair annotations through Terra doesn't create links for case and control samples in the workspace. Any pair level workflow complains that case and control samples are not found.
Only if pair metadata uploaded through Firecloud it creates those links and workflow runs without the problem.
Encountered this bug already twice.
Example of the view from Firecloud after uploading pair.tsv through Terra:
View of those samples:
Comments
10 comments
Hello Liudmila -
I was able to replicate this bug and will be creating an Issue ticket to get it resolved.
Thank you!
Hello Sushma,
Thank you very much for helping with this issue.
Just wanted to add that uploading pair metadata through TSV file will also not create a link to a file. For example, if there is a file that needs to be on a pair level uploading TSV metadata creates
an annotation for this file but the field with the path to the file would be empty.
Uploading Sample.tsv metadata also does not create a link for the participant.
Hello Luda,
I have updated the issue ticket with this new information after confirming with a test workspace of my own. Thank you for contributing your feedback!
Hi,
I am also facing this issue. I uploaded participant and samples tsv info files. However, when I am uploading the pairs tsv file if I click on the button below
If gives me the following errors:
How to go about it?
Thanks,
Sahar
Hi Sahar,
In Terra, you have to make sure that your Participant table is uploaded first, then samples, and then you can upload the pairs table. It looks like you have done this already and on the last upload of your pair table you are seeing the above errors.
Can you expand the errors under Cause1 and Cause2 and share the screenshot as well as screenshots of what your current data table looks like? Screenshots of your .tsv files would also be useful. I do think that if this is uploaded successfully the Tool you are trying to run will also work successfully.
Thanks.
Hello Sahar,
Were you able recently to upload metadata through Terra so that it links pair to case and control samples?
We are still encountering this issue. And, yes, we first upload Participant.tsv, then Sample.tsv and only then Pair.tsv.
I can create a test set for you to replicate this bug.
Thank you,
Luda
Hello Liudmila,
We are trying to replicate the error and still cannot seem to do so. We first create a participant.tsv, sample.tsv, and then pair.tsv and upload them to Terra is that same order. Each time we upload a .tsv, we select the button that notes "Create participant, sample, and pair associations".
Once these files are uploaded, we are able to run a test workflow that uses pair data as input. The Terra platform does not create the links visibly in the Data Table the way it appears in FireCloud but the test workflow is working.
Can you confirm which workflow you are using?
Sushma
Hi Sushma,
I'm also experiencing the same error that Luda and Sahar ran into. I've uploaded my participant.tsv and then my sample.tsv to Terra, always selecting the button to create associations. When I try to upload my pair.tsv and click on the button to create associations, I get this error:
There is no text when I expand the cause.
My pair.tsv contains the columns in the order specified here https://software.broadinstitute.org/firecloud/documentation/article?id=9772.
How can I fix this error?
Thanks,
Gwen
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