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a3m msa input for colabfold #174

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a3m msa input for colabfold #174

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@vagkaratzas vagkaratzas commented Aug 5, 2024

This is an initial PR, mostly to showcase the changes needed to make an MSA input work, starting with colabfold, and then continue by building upon this.
The tricky part will be to test the initial input samplesheet.csv for both options; fasta sequence files, and/or msa folder with a3m MSA files.
The COLABFOLD_BATCH module conveniently works the same with both fasta and msa inputs.

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github-actions bot commented Aug 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2a9a458

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

❗ 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 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 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 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 2024-08-05 14:27:53

@luisas luisas mentioned this pull request May 7, 2025
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