IS anoyne else getting the following error when ru...
# modulesj
James Fellows Yates
05/08/2026, 1:38 PMIS anoyne else getting the following error when running unrelated tests:
James Fellows Yates
05/08/2026, 1:39 PM@Jonathan Manning @Toni Hermoso Pulido it looks like you guys merged this but with failing tests: https://github.com/nf-core/modules/actions/runs/25489958950
is there some context to that?
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Jonathan Manning
05/08/2026, 1:40 PMI preliminarily approved it since we had a green light a couple of commits earlier. Didn't merge it...
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James Fellows Yates
05/08/2026, 1:40 PMSorry yes, I meant you reviewed
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Toni Hermoso Pulido
05/08/2026, 1:41 PMj
James Fellows Yates
05/08/2026, 1:41 PMNo that's noth te test that's broken
James Fellows Yates
05/08/2026, 1:41 PMThe GPU tests didn't run at all
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Toni Hermoso Pulido
05/08/2026, 1:41 PMHey! I assume that was that
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James Fellows Yates
05/08/2026, 1:42 PMand the file was completely borked
James Fellows Yates
05/08/2026, 1:42 PMJames Fellows Yates
05/08/2026, 1:42 PMA fix I think
James Fellows Yates
05/08/2026, 1:42 PM(context: I couldn't run my own tests because nf-test picked up the fault test and died)
James Fellows Yates
05/08/2026, 1:42 PMHrm doesn't seem to be enough...
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Jonathan Manning
05/08/2026, 1:43 PMWant me to sort it James? Shouldn't have approved before the tests ran.
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James Fellows Yates
05/08/2026, 1:43 PMYes please...
James Fellows Yates
05/08/2026, 1:43 PMThat file seems to ghave more issues than the second
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Jonathan Manning
05/08/2026, 1:43 PMI'll make your pr pass
❤️ 1
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James Fellows Yates
05/08/2026, 1:44 PMIU suspect this will block anyone who syncs the modules
mastert
Toni Hermoso Pulido
05/08/2026, 1:44 PMMy fault, sorry about that
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James Fellows Yates
05/08/2026, 1:44 PMfrom when the module was merged in
James Fellows Yates
05/08/2026, 1:44 PMIt's OK things happen! I was just checking first I didn't miss some context and maybe I was doing something wrong
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Toni Hermoso Pulido
05/08/2026, 1:45 PMThere was still a Conda time out after 2 h , @Jonathan Manning - curiously one only. But that's unrelated I think
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James Fellows Yates
05/08/2026, 1:45 PMYEah tha'ts an allowable thing to skip (you can probably add that to the 'ignore conda' list that is somewhere
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Jonathan Manning
05/08/2026, 1:46 PMOriginally it was because Toni was trying to download monster-big model files, but thought we'd fixed that...
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Evangelos Karatzas
05/08/2026, 1:49 PMmust be this, right?
Copy code
process {
input[0] = [
[ id:'test_model' ],
"mradermacher/tiny-gemma-test-i1-GGUF",
"tiny-gemma-test.i1-Q4_K_M.gguf"
]
]Evangelos Karatzas
05/08/2026, 1:49 PMan extra
]j
James Fellows Yates
05/08/2026, 1:50 PMTHere is a second error
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Evangelos Karatzas
05/08/2026, 1:50 PMit's usually a missing coma..
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James Fellows Yates
05/08/2026, 1:50 PMimage.png
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Evangelos Karatzas
05/08/2026, 1:51 PMAh sorry, just saw you already flagged that bracket :p
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Toni Hermoso Pulido
05/08/2026, 1:56 PMCould it be something with quotes ' vs " ?
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James Fellows Yates
05/08/2026, 1:57 PMPossibly
James Fellows Yates
05/08/2026, 1:57 PMI count x4
'''"""j
Jonathan Manning
05/08/2026, 1:58 PMj
James Fellows Yates
05/08/2026, 1:58 PMAh found it
James Fellows Yates
05/08/2026, 1:58 PMExactly
James Fellows Yates
05/08/2026, 1:58 PMThank you Jon-Claude
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🤣 1
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Jonathan Manning
05/08/2026, 1:58 PMvan dam
100 rainbow 1
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🤣 1
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Mahesh Binzer-Panchal
05/08/2026, 1:59 PMI'm getting
Copy code
nf-core modules test krakenuniq/build --profile docker
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 4.0.2 - <https://nf-co.re>
INFO Generating nf-test snapshot
Displaying nf-test output
╭───────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ──────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ 🚀 nf-test 0.9.2 │
│ <https://www.nf-test.com> │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr │
│ │
│ Error: Syntax errors in nf-test config file: java.lang.RuntimeException: Plugin'nft-anndata' found, but version 0.4.1 not found. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Displaying nf-test error
INFO Generating nf-test snapshot again to check stability
Displaying nf-test output
╭───────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ──────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ 🚀 nf-test 0.9.2 │
│ <https://www.nf-test.com> │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr │
│ │
│ Error: Syntax errors in nf-test config file: java.lang.RuntimeException: Plugin'nft-anndata' found, but version 0.4.1 not found. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Displaying nf-test error
CRITICAL Ran, but found errors:
- nf-test failed
- nf-test failedj
James Fellows Yates
05/08/2026, 2:00 PMWhere is that @Mahesh Binzer-Panchal? locally?
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Mahesh Binzer-Panchal
05/08/2026, 2:00 PMyes
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James Fellows Yates
05/08/2026, 2:00 PMWhenever I get that I just delete
.nf-test/m
Mahesh Binzer-Panchal
05/08/2026, 2:02 PMNow I get what you get:
Copy code
% nf-core modules test krakenuniq/build --profile docker
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 4.0.2 - <https://nf-co.re>
INFO Generating nf-test snapshot
Displaying nf-test output
╭───────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ──────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ 🚀 nf-test 0.9.2 │
│ <https://www.nf-test.com> │
│ (c) 2021 - 2024 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/0.6.1/nft-bam-0.6.1.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-fastq/0.1.0/nft-fastq-0.1.0.jar │
│ Load .nf-test/plugins/nft-utils/0.0.9/nft-utils-0.0.9.jar │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar │
│ Error: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/modules/nf-core/llamacpppython/run/tests/main.gpu.nf.test: 1: Unexpected input: '{' @ line 1, column 18. │
│ nextflow_process { │
│ ^ │
│ │
│ 1 error │
│ │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Displaying nf-test error
INFO Generating nf-test snapshot again to check stability
Displaying nf-test output
╭───────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ──────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ 🚀 nf-test 0.9.2 │
│ <https://www.nf-test.com> │
│ (c) 2021 - 2024 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/0.6.1/nft-bam-0.6.1.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-fastq/0.1.0/nft-fastq-0.1.0.jar │
│ Load .nf-test/plugins/nft-utils/0.0.9/nft-utils-0.0.9.jar │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar │
│ Error: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/modules/nf-core/llamacpppython/run/tests/main.gpu.nf.test: 1: Unexpected input: '{' @ line 1, column 18. │
│ nextflow_process { │
│ ^ │
│ │
│ 1 error │
│ │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Displaying nf-test error
CRITICAL Ran, but found errors:
- nf-test failed
- nf-test failed
(j
Jonathan Manning
05/08/2026, 2:03 PMJames' PR passing anyway, took the liberty of merging it
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James Fellows Yates
05/08/2026, 2:19 PMimage.png
😂 1
🤣 4
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Jonathan Manning
05/08/2026, 2:19 PMOh gawwd
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James Fellows Yates
05/08/2026, 2:20 PMyou knew it was coming
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Phil Ewels
05/08/2026, 3:35 PMShouldn't have approved before the tests ran.Nah this should be fine, up to the merger to check tests, not approver
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Jose Espinosa-Carrasco
05/08/2026, 3:41 PMhaha I never now if I should wait