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[WIP] Feature comet config#178

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julianu wants to merge 12 commits into
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feature_comet_config
Open

[WIP] Feature comet config#178
julianu wants to merge 12 commits into
devfrom
feature_comet_config

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@julianu

@julianu julianu commented Jul 2, 2026

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This introduces the cometconfig module
(but first #170 ident_dda must be merged)

@julianu julianu requested a review from a team July 2, 2026 14:57
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2622e25

+| ✅ 196 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗  21 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: If applicable, add a list of additional contributors here
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in main.nf.test: Add tags for all modules used within this subworkflow. Example:
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in meta.yml: # Add a description of the module and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
  • pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-macproqc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-macproqc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-macproqc_logo_dark.png
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-07-10 10:00:25

@julianu julianu mentioned this pull request Jul 2, 2026
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di-hardt
di-hardt requested changes Jul 9, 2026
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there should be a test case to make sure the comet.params file under assets has the same version as comet. otherwise a comet update could brake the pipeline when the default config was not updated but used.

Comment thread modules/local/cometconfig/templates/adjust_comet_params.py

@di-hardt di-hardt Jul 9, 2026

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this is part of the helper python module, could you use it?

@julianu julianu Jul 10, 2026

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The test case checks the adjusted params file for identity (using a hash).
If the provided asset file is updated, the test needs to be updated, which is intended. Newer versions of comet also don't break with older files if only the version is wrong. They just break if they don't understand the parameters.

Comet is not used yet in this PR (was accidentally added but removed now again).

I am using the template function and remove the function in the python helper module. Here, the template works nicely (as it is short enough and only used as nf-core [local] module).

@julianu julianu requested a review from di-hardt July 10, 2026 10:04
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@julianu @di-hardt