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feat: civicpy/annotate module#11079

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emmcauley wants to merge 3 commits intonf-core:masterfrom
fulcrumgenomics:em_civipy_annotate
Draft

feat: civicpy/annotate module#11079
emmcauley wants to merge 3 commits intonf-core:masterfrom
fulcrumgenomics:em_civipy_annotate

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@emmcauley emmcauley commented Mar 27, 2026 •
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PR checklist

Closes #11076.

This module adds CIVICpy, an analysis toolkit and SDK for extracting and analyzing knowledge from the CIViC knowledgebase. Tests are added.

⚠️ This PR is waiting on a new release of civicpy to fix the backports dependency.

Traceback (most recent call last):
  File "/usr/local/bin/civicpy", line 6, in <module>
    from civicpy.cli import cli
  File "/usr/local/lib/python3.12/site-packages/civicpy/cli.py", line 4, in <module>
    from civicpy import LOCAL_CACHE_PATH, civic
  File "/usr/local/lib/python3.12/site-packages/civicpy/civic.py", line 13, in <module>
    from backports.datetime_fromisoformat import MonkeyPatch
ModuleNotFoundError: No module named 'backports.datetime_fromisoformat'

Trying to add backports into the wave container build fails even if they're both from pip.

Also logged an issue on the civicpy repo here.

  • 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

@emmcauley emmcauley marked this pull request as ready for review March 27, 2026 18:46
@emmcauley emmcauley force-pushed the em_civipy_annotate branch 2 times, most recently from 932b1eb to ef3d2d1 Compare March 27, 2026 19:12
@emmcauley emmcauley force-pushed the em_civipy_annotate branch from ef3d2d1 to 249aa89 Compare March 27, 2026 22:26
emmcauley
emmcauley commented Mar 27, 2026
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Comment thread modules/nf-core/civicpy/annotate/main.nf Outdated
Comment on lines +7 to +8
? 'https://depot.galaxyproject.org/singularity/civicpy:5.2.0--pyhdfd78af_0'
: 'docker.io/griffithlab/civicpy:v5.2.0' }"
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@emmcauley emmcauley Mar 27, 2026

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these are non-standard because I ran into issues building the wave container for docker + singularity

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@famosab famosab Apr 13, 2026

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We have a quay.io repository for custom docker containers. It is a recommendation to upload them there so that we stay independent of third parties that might delete the images. See the docs for more info. You can request the upload via #request-core in the nf-core slack. I think its fine to store it there until they resolve the issue on their side :)

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@emmcauley emmcauley Apr 14, 2026

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I've requested this in Slack; feel free to add more context if it's lacking! The tests won't pass until we get the custom Docker container but in the meantime, I think I've addressed your other feedback. thanks for the review!

@emmcauley emmcauley marked this pull request as draft April 7, 2026 13:56
@emmcauley emmcauley added the new module Adding a new module label Apr 10, 2026
famosab
famosab reviewed Apr 13, 2026
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Nice! I am also interested in having civic added to nf-core so I already added some feedback to help with the module development :)

Comment thread modules/nf-core/civicpy/annotate/tests/main.nf.test Outdated
Comment thread modules/nf-core/civicpy/annotate/tests/nextflow.config Outdated
Comment thread modules/nf-core/civicpy/annotate/main.nf Outdated
Comment on lines +7 to +8
? 'https://depot.galaxyproject.org/singularity/civicpy:5.2.0--pyhdfd78af_0'
: 'docker.io/griffithlab/civicpy:v5.2.0' }"
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@famosab famosab Apr 13, 2026

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We have a quay.io repository for custom docker containers. It is a recommendation to upload them there so that we stay independent of third parties that might delete the images. See the docs for more info. You can request the upload via #request-core in the nf-core slack. I think its fine to store it there until they resolve the issue on their side :)

Comment thread modules/nf-core/civicpy/annotate/main.nf Outdated
Comment thread modules/nf-core/civicpy/annotate/main.nf Outdated
Comment thread modules/nf-core/civicpy/annotate/main.nf Outdated
Comment thread modules/nf-core/civicpy/annotate/main.nf
Comment thread modules/nf-core/civicpy/annotate/meta.yml Outdated
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "civicpy_annotate"

description: A python client and analysis toolkit for the Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase
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@famosab famosab Apr 13, 2026

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Can you be more specific for annotate here?

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@emmcauley emmcauley Apr 14, 2026

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revised

Comment thread modules/nf-core/civicpy/annotate/main.nf

civicpy annotate-vcf \\
--input-vcf ${vcf} \\
--output-vcf ${prefix}.vcf \\
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@famosab famosab Apr 13, 2026

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We usually want the vcf files to be bgzipped if possible

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@emmcauley emmcauley Apr 14, 2026

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I've added htslib + bgzip

Comment thread modules/nf-core/civicpy/annotate/environment.yml
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@famosab famosab Apr 13, 2026

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Conda probably has the same issue as the biocontainer / wave container?

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@emmcauley emmcauley Apr 14, 2026

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yep! Hopefully should be fixed in the next release.

@emmcauley emmcauley mentioned this pull request Apr 14, 2026
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@emmcauley emmcauley force-pushed the em_civipy_annotate branch from 8db2250 to a155533 Compare April 14, 2026 17:16
@emmcauley emmcauley force-pushed the em_civipy_annotate branch from a155533 to e4d82ef Compare April 14, 2026 17:26
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new module: civicpy/anotate

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