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Produce an interactive html report for the predicted strucures #181

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Produce an interactive html report for the predicted strucures #181

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ziadbkh
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@ziadbkh ziadbkh commented Oct 2, 2024

Creating an interactive html report to show the predicted structures and plddt plots for ALPHAFOLD, ESMFOLD, and COLABFOLD.

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).

JoseEspinosa and others added 25 commits July 30, 2024 17:54
@JoseEspinosa
Pin zenodo doi in readme
8cfcb4c
@JoseEspinosa
Update changelog for v1.2.0dev
0673505
@JoseEspinosa
bump dev version in images
f2247ae
@JoseEspinosa
bump dev in multiqc_config
3986454
@JoseEspinosa
Merge pull request nf-core#173 from JoseEspinosa/bump_1.2.0dev
4ace60d 
Bump version 1.2.0 dev
@JoseEspinosa
Fix uppercase model preset
bfd3c76
@JoseEspinosa
Update changelog
4769bee
@JoseEspinosa
Fix instances of alphafold2_ptm
4ca5fdc
@JoseEspinosa
Fix condition to run MULTIFASTA_TO_CSV when executing colabfold serve…
02babc4 
…r local
@JoseEspinosa
Merge pull request nf-core#175 from JoseEspinosa/fixes
c3c7cc7 
Fix uppercase model preset "alphaFold2-ptm"
accepting mutltiple models
b520b9b
accepting mutltiple models
78ba288
update usage
e7b4f06
update docs - usage and output
0bb9d9d
update change log
080c16f
lint minor fixes
fbe5203
lint fixes
dc3bf4f
add results visulisation
3d02fc5
configure the reports
586798c
rename esmfold output pdb
6985dcd
@minh-biocommons
average, tooltip & msa png
81e877e
@ziadbkh
Merge pull request #1 from minh-biocommons/visualisation
411816b 
average, tooltip & msa png
rename version file name
7eeee46
caluclate plddt using the averages
f6193b8
update visualisation report
84718af
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github-actions bot commented Oct 2, 2024

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @ziadbkh,

It looks like this pull-request is has been made against the ziadbkh/proteinfold master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the ziadbkh/proteinfold dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@ziadbkh ziadbkh closed this Oct 2, 2024
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github-actions bot commented Oct 2, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 84718af

+| ✅ 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 2024-10-02 06:09:44

@JoseEspinosa JoseEspinosa mentioned this pull request Oct 4, 2024
Merged
11 tasks
@JoseEspinosa JoseEspinosa changed the title Produce an interactive html report for the predecited strucures Produce an interactive html report for the predicted strucures Oct 8, 2024
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3 participants
@ziadbkh @JoseEspinosa @minh-biocommons