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Fix incorrect references to RAPID-TOL#472

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DLBPointon wants to merge 13 commits into
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471-fixes
Open

Fix incorrect references to RAPID-TOL#472
DLBPointon wants to merge 13 commits into
devfrom
471-fixes

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@DLBPointon DLBPointon commented May 13, 2026

Fixes related to #471

  • Fixes to usage.md where RAPID_TOL was incorrectly down as RAPID-TOL
  • Over zealous required values in the schema, stopping people from just not adding things like kmer_profile information to the input file.
  • Due to the above, YAML_INPUT was not treating null values correctly
    • Fixes started with kmer_profile data.

@DLBPointon DLBPointon self-assigned this May 13, 2026
@DLBPointon DLBPointon moved this from Todo to In progress in WRAP team board May 13, 2026
@DLBPointon DLBPointon marked this pull request as draft May 13, 2026 10:42
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sanger-tolsoft commented May 13, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
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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github-actions Bot commented May 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a7a299e

+| ✅ 220 tests passed       |+
#| ❔  30 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  10 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.4.7
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • system_exit - System.exit in treeval.nf: System.exit(1) [line 113]
  • system_exit - System.exit in treeval.nf: System.exit(1) [line 120]

❔ Tests ignored:

  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-05-19 09:28:26

@DLBPointon DLBPointon mentioned this pull request May 13, 2026
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DLBPointon commented May 13, 2026

We would be able to have much better control of the required data per mode if params.mode were to move into the yaml rather than the cli.

@DLBPointon DLBPointon mentioned this pull request May 13, 2026
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@DLBPointon DLBPointon marked this pull request as ready for review May 19, 2026 09:25
muffato
muffato reviewed May 19, 2026
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(I know this PR is only about documenting the actual process, so this is not in scope of this PR. Something else to consider). I think the BED etc files should be compressed as they can be quite big otherwise. I understand that the "big" versions are binary and less practical to use, but a bgzip is already quite good

Comment thread CHANGELOG.md
### Parameters
| Old Parameter | New Parameter |
| ------------- | ------------- |
| - | --kmer_length |
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@muffato muffato May 19, 2026

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Suggested change
| - | --kmer_length |
| | --kmer_length |

Comment thread assets/local_testing/params.json
@@ -0,0 +1,7 @@
{
"input": "./assets/local_testing/grTriPseu1.yaml",
"outdir": "TESTING",
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@muffato muffato May 19, 2026

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I would recommend outdir to not be in the file; only use the file for input params.

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nikostr commented May 20, 2026

Would it make sense to get rid of the 'punchlist' nomenclature as a part of this PR, and replace that word with short descriptions of what the files contain?

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