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@fellen31 fellen31 commented Dec 10, 2025

PR checklist

Missed this in #9541.

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@fellen31 fellen31 force-pushed the add-outputs-to-trgt-merge branch 3 times, most recently from 69558f2 to 375806f Compare December 10, 2025 14:37
@fellen31 fellen31 force-pushed the add-outputs-to-trgt-merge branch from 375806f to b54e482 Compare December 10, 2025 14:42
@fellen31 fellen31 marked this pull request as ready for review December 10, 2025 14:48
Comment on lines +236 to +257
"index": [
[
{
"id": "test"
},
"test.bcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"vcf": [
[
{
"id": "test"
},
"test.bcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions_trgt": [
[
"TRGT_MERGE",
"trgt",
"5.0.0-e9acee0"
]
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are there suppossed to be duplicated entries here, once with a key and once with an index?

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I don't really understand why there are duplicate entries though, I just have

        then {
            assertAll(
                { assert process.success },
                { assert snapshot(process.out).match() }
            )
        }

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looks to be standard, sorry. will think about how we can avoid that...

@fellen31 fellen31 added this pull request to the merge queue Dec 10, 2025
Merged via the queue into nf-core:master with commit 528ae7a Dec 10, 2025
41 checks passed
@fellen31 fellen31 deleted the add-outputs-to-trgt-merge branch December 10, 2025 19:24
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2 participants