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Change uniclust30 to uniref30 path when using the full BFD database in Alphafold2 #97

Merged
merged 2 commits into from
May 16, 2023
Merged

Change uniclust30 to uniref30 path when using the full BFD database in Alphafold2 #97

merged 2 commits into from
May 16, 2023

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athbaltzis
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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/proteinfold branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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 May 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b7f59db

+| ✅ 157 tests passed       |+
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowProteinfold.groovy
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 check_samplesheet.py: Update the script to check the samplesheet
  • pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
  • pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet
  • 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.

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-16 13:02:15

@athbaltzis athbaltzis linked an issue May 16, 2023 that may be closed by this pull request
PDBMMCIF download error #96
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JoseEspinosa
JoseEspinosa approved these changes May 16, 2023
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Awesome!

@JoseEspinosa JoseEspinosa merged commit cc4145d into nf-core:dev May 16, 2023
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JoseEspinosa commented May 16, 2023 •
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Will give it a try right now!

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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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PDBMMCIF download error
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@athbaltzis @JoseEspinosa