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Is there anyone who could try a fresh nf-test run ...
# help
j
Is there anyone who could try a fresh nf-test run (i.e. where there are no plugins installed yet?)? Or alternatively try to update their plugins with 
nf-test update-plugins
m
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nf-test update-plugins

🚀 nf-test 0.9.5
<https://www.nf-test.com>
Please cite: <https://doi.org/10.1093/gigascience/giaf130>
(c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-bam/0.7.0/nft-bam-0.7.0.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Load .nf-test/plugins/nft-utils/1.2.1/nft-utils-1.2.1.jar
Plugins updated.
??
j
Can you try downloading a new plugin you don't have?
Or wipe your `.nf-test`folder and rub updating again?
m
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(preprocessing) ➜  nf-cmgg-preprocessing git:(chore/fix-tests) rm -rf .nf-test
(preprocessing) ➜  nf-cmgg-preprocessing git:(chore/fix-tests) nf-test update-plugins

🚀 nf-test 0.9.5
<https://www.nf-test.com>
Please cite: <https://doi.org/10.1093/gigascience/giaf130>
(c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-bam/0.7.0/nft-bam-0.7.0.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Load .nf-test/plugins/nft-utils/1.2.1/nft-utils-1.2.1.jar
Plugins updated.
m
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nf-test update-plugins

:rocket: nf-test 0.9.5
<https://www.nf-test.com>
Please cite: <https://doi.org/10.1093/gigascience/giaf130>
(c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-anndata/0.4.1/nft-anndata-0.4.1.jar
Load .nf-test/plugins/nft-bam/0.7.0/nft-bam-0.7.0.jar
Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar
Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar
Load .nf-test/plugins/nft-fasta/1.0.0/nft-fasta-1.0.0.jar
Load .nf-test/plugins/nft-fastq/0.1.0/nft-fastq-0.1.0.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Load .nf-test/plugins/nft-utils/1.2.1/nft-utils-1.2.1.jar
Plugins updated.
after I wiped .nf-test
j
Dafuq
🤣 1
m
works fine
j
So my issue from yesterday has been replicaated by @oliviercoen
(see # nf-test)
What versions of java are you guys using?
m
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java --version
openjdk 17.0.18 2026-01-20 LTS
OpenJDK Runtime Environment Zulu17.64+17-CA (build 17.0.18+8-LTS)
OpenJDK 64-Bit Server VM Zulu17.64+17-CA (build 17.0.18+8-LTS, mixed mode, sharing)
m
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(preprocessing) ➜  nf-cmgg-preprocessing git:(chore/fix-tests) java -version
openjdk version "25.0.2" 2026-01-20 LTS
OpenJDK Runtime Environment Zulu25.32+21-CA (build 25.0.2+10-LTS)
OpenJDK 64-Bit Server VM Zulu25.32+21-CA (build 25.0.2+10-LTS, mixed mode, sharing)
j
Ok one more test: delete 
.nf-test
to make sure you have no plugin jars
Then run a test so nf-test downloads it again
m
did that before already
m
me too
j
Ffs
o
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java --version
openjdk 17.0.10 2024-01-16
OpenJDK Runtime Environment Temurin-17.0.10+7 (build 17.0.10+7)
OpenJDK 64-Bit Server VM Temurin-17.0.10+7 (build 17.0.10+7, mixed mode, sharing)
j
OH
HOLD UP
We have the same version @oliviercoen
😮 1
m
time for sdkman/mise 😉
👍 1
m
I use a pixi env 🤷🏻
👍 1
j
Brb meeting
o
it deserves to be told widely to the community, since a lt of people may have openjdk <= 17.0.10
m
do any of those services use PHP? 😅
o
the fixes for PHP were only serverside, but it may impact client requests
in the nextflow installation doc, the default version that is advised is 
17.0.10-tem
: nf-co.re/docs/usage/installation
Ok, I confirm it works after updating java to 17.0.20-tem:
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sdk install java 17.0.20-tem
(NOTE: the 
.nf-test
folder needs to be removed priori to launching 
nf-test test
again)
p
Out of curiosity, how do you end up with such an outdated java?
m
James works (worked?) with ancient DNA, so it’s fitting to use ancient software?
😁 2
m
i use the same as the CI for testing purposes
o
Because it's the version that is pinned both in the Nextflow website: docs.seqera.io/nextflow/install and in the nf-core website: nf-co.re/docs/usage/installation It's supposed to work well
p
Thanks, made a PR for nf-core at least.
❤️ 1
✅ 1
s
James works (worked?) with ancient DNA, so it’s fitting to use ancient software? (edited)
I would imagine there isn't much call for ancient DNA analysis in AstraZeneca
sad cowboy 1
😆 1
m
People are getting older and older 👴🏻
😁 2
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