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Update reviewer comments#99

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vagkaratzas merged 8 commits intodevfrom
update-reviewer-comments
May 7, 2026
Merged

Update reviewer comments#99
vagkaratzas merged 8 commits intodevfrom
update-reviewer-comments

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@vagkaratzas vagkaratzas commented May 7, 2026

Mainly typo fixes + a wrong full_test data path fix.

  • hmmsearch module update
  • utils_ nf-core subworkflows updates

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/proteinannotator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (e.g. nf-test test */local --profile=~test,docker for all new local tests).
  • Check for unexpected warnings in debug mode (nf-test test */local --profile=~test,docker,debug).
  • 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).

@vagkaratzas vagkaratzas requested review from Aratz and pinin4fjords May 7, 2026 12:56
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github-actions Bot commented May 7, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5da123e

+| ✅ 226 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/ci.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: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-07 13:11:26

pinin4fjords
pinin4fjords reviewed May 7, 2026
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AI-assisted review (Claude, on behalf of @pinin4fjords). Thanks for the cleanup — most of the items from the #98 review are addressed here. One small follow-up on the InterProScan flag string.

Comment thread nextflow_schema.json Outdated
"interproscan_enableprecalc": {
"type": "boolean",
"help_text": "This increases the speed of functional annotation with InterProScan by pre-calculating matches found in the UniProtKB, thereby identifying unique matches in the query sequences for faster annotation. By default this is turned off.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `---diasable-precalc`",
"help_text": "This increases the speed of functional annotation with InterProScan by pre-calculating matches found in the UniProtKB, thereby identifying unique matches in the query sequences for faster annotation. By default this is turned off.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `---disable-precalc`",
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Severity: low - the diasable -> disable fix is in, but the leading --- (three dashes) is still there. The actual InterProScan flag is --disable-precalc (two dashes), which is what conf/modules.config:173 correctly passes.

Suggested change
"help_text": "This increases the speed of functional annotation with InterProScan by pre-calculating matches found in the UniProtKB, thereby identifying unique matches in the query sequences for faster annotation. By default this is turned off.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `---disable-precalc`",
"help_text": "This increases the speed of functional annotation with InterProScan by pre-calculating matches found in the UniProtKB, thereby identifying unique matches in the query sequences for faster annotation. By default this is turned off.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--disable-precalc`",

@vagkaratzas vagkaratzas merged commit 696ad48 into dev May 7, 2026
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@vagkaratzas vagkaratzas deleted the update-reviewer-comments branch May 7, 2026 13:18
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@Aratz Aratz Awaiting requested review from Aratz

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