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Docs fix: 'AlphaFold2-ptm' -> 'alphafold2_ptm' #207

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Docs fix: 'AlphaFold2-ptm' -> 'alphafold2_ptm' #207

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alex000kim
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@alex000kim alex000kim commented Oct 28, 2024 •
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Docs in https://nf-co.re/proteinfold/1.1.1
refer to --colabfold_model_preset "AlphaFold2-ptm" which results in an error below:

$ nextflow run nf-core/proteinfold -r 1.1.1 \
    --input samplesheet.csv \
    --outdir my_results \
    --mode colabfold \
    --colabfold_server local \
    --num_recycle 3 \
    --colabfold_model_preset "alphafold2_ptm" \
    --use_gpu true

...
ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --colabfold_model_preset: 'AlphaFold2-ptm' is not a valid choice (Available choices (5 of 6): auto, alphafold2, alphafold2_ptm, alphafold2_multimer_v1, alphafold2_multimer_v2, ... )

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github-actions bot commented Oct 28, 2024 •
edited by nf-core-bot
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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: 2.14.1.
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.

@alex000kim alex000kim changed the base branch from master to dev October 28, 2024 02:14
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github-actions bot commented Oct 28, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3415c26

+| ✅ 205 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • 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 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-28 15:32:54

@JoseEspinosa
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Hi @alex000kim and thanks for contributing!
This was already added to the pipeline but seems that for some reason you were not getting these changes in your fork, we have updated and as you can see your changes are gone, thus, I will close your PR now.

@alex000kim
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Oh right, I should've forked from dev not master

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3 participants
@alex000kim @JoseEspinosa @ewels