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Fix uppercase model preset "alphaFold2-ptm" #175

Merged
merged 4 commits into from
Aug 7, 2024
Merged

Fix uppercase model preset "alphaFold2-ptm" #175

merged 4 commits into from
Aug 7, 2024

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JoseEspinosa
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PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

@JoseEspinosa JoseEspinosa marked this pull request as ready for review August 6, 2024 14:11
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github-actions bot commented Aug 6, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 02babc4

+| ✅ 195 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • nextflow_config - Config manifest.version should end in dev: 1.1.1
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-07 13:18:12

vagkaratzas
vagkaratzas requested changes Aug 6, 2024
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workflows/colabfold.nf Outdated
@@ -91,7 +91,7 @@ workflow COLABFOLD {
//
// MODULE: Run mmseqs
//
if (params.colabfold_model_preset != 'AlphaFold2-ptm') {
if (params.colabfold_model_preset != 'alphaFold2-ptm') {
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Should we also add here:
&& params.colabfold_model_preset != 'alphafold2'
as in the webserver mode? Or is it different for some reason?
Which cases does the module MULTIFASTA_TO_CSV need to run for?

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I really thought it was different but discussing with @athbaltzis it seems to be just a bug since alphafold2 is not used so often, now is fixed. Good spot! 😄

workflows/colabfold.nf Outdated
@@ -91,7 +91,7 @@ workflow COLABFOLD {
//
// MODULE: Run mmseqs
//
if (params.colabfold_model_preset != 'AlphaFold2-ptm') {
if (params.colabfold_model_preset != 'alphaFold2-ptm') {
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It should be alphafold2_ptm, all lowercase, with underscore for the latest version I think.

@JoseEspinosa JoseEspinosa merged commit c3c7cc7 into nf-core:dev Aug 7, 2024
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@vagkaratzas vagkaratzas vagkaratzas approved these changes

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@JoseEspinosa @vagkaratzas