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Hi, still need a review/approval from the <!subtea...
# methylong
j
Hi, still need a review/approval from the <!subteam^S016E36N7TQ> on the actual PR (not pseudo): https://github.com/nf-core/methylong/pull/6 woohoo
j
you can also ask in #C08K66XCZSL I don't have time this week but could have a look next week if no one else can do it earlier
👍 1
j
thank you!
@Júlia Mir could I then assign u as the reviewer? :))
j
yes 👍🏻
mewhiq 1
j
@Júlia Mir thanks a lot for reviewing ^^ is there a way to access to seqera platform to check aws progress? it failed instantly in the last run and im wondering what happened 🤔
j
I can't find a methylong run in the platform, where did you see the filure?
j
the log is here: https://github.com/nf-core/methylong/actions/runs/14612281050/job/40992563521 but i am rerunning the tests again after resolving the comments, so a new one will start soon
also not really sure why it was skipped instead
j
I think there is an error in the github action
this is the template version of this file with the fix, it's on nf-core/tools dev so not released yet, but you can already copy this file to have it updated
I am also trying to launch this test from seqera manually
r
Are you doing testing the full size tests?
I am goign through the lst of all the missing ones at the moment. Want me to add this one in?
j
this is the run I just started
it's a first release so I don't think there's anything missing yet, or do you mean something different @Rike Hanssen?
r
I just meant. I am submitting tons of runs at the moment and can add in another one if necessary
j
ah ok! I just added this one, but will let you know if something fails 😄
j
okay, i will try with the new template version
r
Can we move the test files to our s3 bucket:
Copy code
Can't stage file <https://42basepairs.com/download/s3/ont-open-data/giab_2025.01/basecalling/sup/HG002/PAW70337/calls.sorted.bam> -- reason: Connection reset
j
i used the template u suggested here, but seems like theres a problem with triggering the test, the error i got:
Copy code
actions_awsfulltest: .github/workflows/awsfulltest.yml is not triggered      │
│ correctly
solved by adding this bit in:
Copy code
pull_request:
    branches:
      - main
      - master
j
True! This would be only to run it on this PR but you should remove it before merging
j
ah okay so once the aws tests are done, I will remove this before release :))
hii @Rike Hanssen, is it doable to move the dataset? or should i use a different data source?
there is also a link directly to the s3 bucket: s3://ont-open-data/giab_2025.01/basecalling/sup/HG002/PAW71238/calls.sorted.bam would changing to this help?
r
yes we can move those over.
We like to put the data into our bucket to have more control and not be dependent on others moving it + it make any CE permissions easier to deal with
I am not sure I can get to it today. Does anyone else on the core team have time?
Can you give me a list of files please with their s3 paths that you need transferred?
I got a few minutes now 🙂
j
sure, one sec
https://downloads.pacbcloud.com/public/revio/2024Q4/WGS/GIAB_trio/HG003/m84039_241002_000337_s3.hifi_reads.bc2020.bam for pacbio this is not in a s3 bucket I supposed but its on their cloud server, will this work?
just these 2
r
I need to see. what size is it
j
48G
r
😄 ok, I'll try to download and upload it again. Might be a while
j
i will check quickly if theres a s3 bucket available somewhere!
👍 1
found it :))
not exactly the same data, but shouldnt matter so much for run test
will this work? 😁
r
sweet. Yes that should hopefully be ok. In a meeting will try to take a look after
high five 1
j
I managed to copy the files to our bucket, the first one is s3://nf-core-awsmegatests/methylong/HG002_PAW70337_calls.sorted.bam and the second one will be in s3://nf-core-awsmegatests/methylong/HG003_PacBio-Revio_m84039_230928_220759_s4.hifi_reads.bam (it is still uploading)
I have to leave now but let me know if there is any problem or if everything works 😄
j
I will try these paths in the next run, thanks Júlia!
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