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Produce an interactive html report for the predecited strucures #182

Merged
merged 29 commits into from
Oct 4, 2024
Merged

Produce an interactive html report for the predecited strucures #182

merged 29 commits into from
Oct 4, 2024

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ziadbkh
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@ziadbkh ziadbkh commented Oct 2, 2024 •
edited by JoseEspinosa
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Creating an interactive html report to show the predicted structures and plddt plots for ALPHAFOLD, ESMFOLD, and COLABFOLD.

Closes #181

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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Oct 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 62669fe

+| ✅ 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 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 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 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.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-03 23:33:30

JoseEspinosa
JoseEspinosa requested changes Oct 3, 2024
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Awesome!
Only some small suggestions and a question

assets/proteinfold_template.html Show resolved Hide resolved
bin/generat_report.py Outdated Show resolved Hide resolved
main.nf Outdated Show resolved Hide resolved
modules/local/run_alphafold2.nf Outdated Show resolved Hide resolved
bin/extract_output.py Outdated Show resolved Hide resolved
main.nf Outdated Show resolved Hide resolved
modules/local/colabfold_batch.nf Outdated Show resolved Hide resolved
modules/local/run_esmfold.nf Outdated Show resolved Hide resolved
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ziadbkh and others added 6 commits October 4, 2024 09:19
@ziadbkh @JoseEspinosa
rename generate_report.py
f0aaa57 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@ziadbkh @JoseEspinosa
Update modules/local/run_alphafold2.nf
3cf523f 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@ziadbkh @JoseEspinosa
Update bin/extract_output.py
75b048f 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@ziadbkh @JoseEspinosa
Update main.nf
6e0a3a7 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@ziadbkh @JoseEspinosa
Update modules/local/colabfold_batch.nf
114aed8 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@ziadbkh @JoseEspinosa
Update modules/local/run_esmfold.nf
882015c 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
ziadbkh and others added 3 commits October 4, 2024 09:24
JoseEspinosa
JoseEspinosa approved these changes Oct 4, 2024
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Awesome! Thanks a lot! 🚀

@ziadbkh ziadbkh merged commit 7789713 into nf-core:dev Oct 4, 2024
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@JoseEspinosa JoseEspinosa mentioned this pull request Oct 8, 2024
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@ziadbkh @JoseEspinosa @minh-biocommons