Hi, I noticed that the aws workflow results that are published on nf-co.re are missing the report. The process ran during the test and produced a file, but it does not show in the AWS results. Is there some configuration that I missed?

Which report exactly?

genomeassembler is creating a QC report (should be in

report/

) which does not show up here nf-co.re/genomeassembler/…/results-a72d… but all other outputs do?

image.png

I am confused about several things: • I am not sure what the screenshot you pasted is from / what I should take from it. It does not list the folder

report

? • There were two runs on platform: this one was successful, however, I think the merge triggered another test, which failed. I guess the results come from the successful one (disctracted_bernard). The logs seem fine to me, however, also on platform the

outputs

tab lists nothing? • I do not know how to inspect the output bucket via platform; when I look in the task workdir, the report is okay, except that it seems like fonts cannot be fetched from googlefonts?

Sorry - the screenshot is from the AWS S3 Interface. I was confirming the nf-core website was just mirroring the bucket file list. This implies either there was a problem publishing the report directory from the work dir to the final results dir, or IT just didn't execute. When you check on platform: there is nothing in the logs about

failed to publish

? We've there is nothing in date explorer? You should be able to see everything in there I believe

These are the last 3 lines from the log:

[ee/508a90] Submitted process > NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:REPORT (REPORT)
-[nf-core/genomeassembler] Pipeline completed successfully-
WARN: Slack plugin: Failed to add reaction 'white_check_mark': missing_scope (add reactions:write scope to your Slack app)

Ok that does look ok

image.png

🥲

I also know nothing about AWS or platform. If this needs another full_test run, that is fine for me, but I would adapt the test to avoid some AWS specific failures..

do you have it specified in the

tower.yml

?

Nope

ok then platform doesn't know that it should be a report. Can you add it there? Here are the docs on how to docs.seqera.io/platform-cloud/reports/overview#…

Thanks

you can also check any of the bigger pipelines. rnaseq or sarek have a relatively detailed list if you want something to c&p

Just to clarify, this affects the reporting tab in tower right? But does not explain why the

report

folder does not show up in outputs?

yes the reporting tab in tower

Ok, great, then I will update

tower.yml

for now

@Rike Hanssen I think this is a pipeline folder called

report

which is not being published to s3, not Platform features at all..?

ah sorry, saw a screenshot with a missing report tab and didn't read the rest carefully: • Platform Reports: needs tower.yml • Platform OUtputs: needs lineage (can enable at the hackathon) •

results/reports

not being published to AWS: no idea. • wbsite mirroring: nothing broken it sounds like

the

REPORT

process publishes to

reports/

. These warnings are there, but they do not stop the report from rendering, it is created in the workdir (

report.html

)

Thinking about this... maybe you can somehow run the test again, and when getting to the end monitor the logs again and somehow monitor the s3 bucket/work directory?

I will probably run the test again when I do the next patch release