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migrate toulligqc to topic versions#9750

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jdc-eit merged 11 commits intonf-core:masterfrom
eit-maxlcummins:toulligqc_topic_versions
Feb 1, 2026
Merged

migrate toulligqc to topic versions#9750
jdc-eit merged 11 commits intonf-core:masterfrom
eit-maxlcummins:toulligqc_topic_versions

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@eit-maxlcummins eit-maxlcummins commented Jan 22, 2026

Updating toulligqc modules to migrate versions to topic channels.

PR checklist

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

SPPearce
SPPearce reviewed Jan 23, 2026
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The tool seems to be failing on conda? Otherwise it'd be fine.

@jdc-eit jdc-eit requested a review from SPPearce January 29, 2026 18:06
@mashehu
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mashehu commented Jan 29, 2026

@nf-core-bot fix linting

mashehu
mashehu reviewed Jan 29, 2026
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modules/nf-core/toulligqc/environment.yml Outdated
Comment on lines 8 to 11
- conda-forge::numpy<2
- conda-forge::pandas<2.2
- conda-forge::matplotlib<3.9
- conda-forge::plotly=5.24.0
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these need to be fixed versions, not ranges

@jdc-eit jdc-eit requested a review from mashehu January 30, 2026 00:46
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mashehu commented Jan 30, 2026

Is there still a missing dependency for conda?

ImportError: cannot import name 'HfFolder' from 'huggingface_hub'

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jdc-eit commented Jan 30, 2026

Is there still a missing dependency for conda?

ImportError: cannot import name 'HfFolder' from 'huggingface_hub'

That's interesting. I get:

❯ nf-test test modules/nf-core/toulligqc/tests/main.nf.test --profile conda

🚀 nf-test 0.9.3
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar
Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.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-fastq/0.0.1/nft-fastq-0.0.1.jar
Load .nf-test/plugins/nft-utils/0.0.7/nft-utils-0.0.7.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar

Test Process TOULLIGQC

  Test [7fe43052] 'sarscov2 - nanopore sequencing_summary' PASSED (45.011s)
  Test [7acdf825] 'sarscov2 - nanopore sequencing_summary + barcodes' PASSED (45.289s)
  Test [ebd2d1ef] 'sarscov2 - nanopore fastq' PASSED (44.864s)
  Test [b259d144] 'sarscov2 - nanopore bam' PASSED (45.134s)
  Test [d6acfbad] 'sarscov2 - nanopore bam - stub' PASSED (42.65s)

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jdc-eit commented Jan 30, 2026 •
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I wonder if pinning a version would work. Something like - conda-forge::huggingface_hub=0.21.1

mashehu
mashehu approved these changes Jan 30, 2026
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modules/nf-core/toulligqc/meta.yml
@@ -1,4 +1,3 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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@mashehu mashehu Jan 30, 2026

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Please keep this line.

@jdc-eit jdc-eit added this pull request to the merge queue Feb 1, 2026
Merged via the queue into nf-core:master with commit 3a7b650 Feb 1, 2026
29 checks passed
@jdc-eit jdc-eit deleted the toulligqc_topic_versions branch February 1, 2026 21:59
cavenel pushed a commit to cavenel/modules that referenced this pull request Feb 5, 2026
@eit-maxlcummins @jdc-eit
@mashehu @nf-core-bot @cavenel
migrate toulligqc to topic versions (nf-core#9750)
7bb714e 
* migrate toulligqc to topic versions

* Modified conda environment to pass conda profile tests

* [automated] Fix linting with Prettier

* Fix linting issues

* Add Explicit Version fot Huggingface_hub in environment.yml

* Add yaml-language-server schema line

---------

Co-authored-by: jdc-eit <jdiaz@eit.org>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
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@mashehu mashehu mashehu approved these changes

@SPPearce SPPearce Awaiting requested review from SPPearce

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@eit-maxlcummins @mashehu @jdc-eit @SPPearce @nf-core-bot