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Nf core template merge 3.3.2 #159

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SusiJo
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@SusiJo SusiJo commented Sep 11, 2025 •
edited by xXFloBaerXx
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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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/metapep branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Sep 11, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 12a9108

+| ✅ 223 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  23 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • schema_description - No description provided in schema for parameter: igenomes_ignore
  • local_component_structure - finalize_microbiome_entities.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - predict_epitopes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - unify_model_lengths.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - download_proteins.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - unpack_bin_archives.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - create_protein_tsv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - prepare_score_distribution.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - split_pred_tasks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - generate_protein_and_entity_ids.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - merge_predictions_buffer.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - prepare_entity_binding_ratios.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - collect_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - merge_predictions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - check_samplesheet_create_tables.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_entity_binding_ratios.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_score_distribution.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - assign_nucl_entity_weights.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - generate_peptides.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - epytope_show_supported_models.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - process_input.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-10-17 16:54:10

@SusiJo SusiJo force-pushed the nf-core-template-merge-3.3.2 branch 7 times, most recently from 483d499 to cf879e3 Compare September 23, 2025 16:11
@SusiJo SusiJo force-pushed the nf-core-template-merge-3.3.2 branch from cf879e3 to a6d06ad Compare September 23, 2025 16:22
@SusiJo SusiJo force-pushed the nf-core-template-merge-3.3.2 branch from 5648a98 to 6fd50eb Compare September 24, 2025 08:14
@SusiJo SusiJo force-pushed the nf-core-template-merge-3.3.2 branch from 707f034 to db78bce Compare October 14, 2025 11:55
@CaroAMN
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CaroAMN commented Oct 14, 2025

Looks good to me 🙂 👍

skrakau
skrakau reviewed Oct 17, 2025
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Thanks a lot for updating this! I would have a two question or remarks:

  • could you squash your commits at the end? that would keep the commit history clean as there are multiple back-and-forth changes that would be confusing otherwise
  • why did you replace the snapshots from the peptides, proteins and predictions db files and replace it with checking for the number of lines?

The rest looks good!

@SusiJo
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SusiJo commented Oct 17, 2025

Hi,
thanks for the feedback. There is no squash commit enabled here directly, but I can of course do that on the command line.

I changed the file checks for the gzipped files because at some point nf-test created different md5sums when testing locally vs in the ci runners. Checking for the exact number of lines aimed at making sure those files contain the same number of peptides/proteins while ignoring the gzipped headers that can differ.
If you prefer the md5sum check I can also switch this back, but re-creating the snapshots will take a few hours.

@skrakau
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skrakau commented Oct 17, 2025

Did it work to check the differences between the files?

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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@skrakau skrakau skrakau left review comments

@CaroAMN CaroAMN CaroAMN approved these changes

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@SusiJo @CaroAMN @skrakau @nf-core-bot
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