Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update GAS version and reformat reference cluster file. #31

Merged
merged 11 commits into from
Jan 8, 2025
Merged

Update GAS version and reformat reference cluster file. #31

merged 11 commits into from
Jan 8, 2025

Conversation

kylacochrane
Copy link
Contributor

@kylacochrane kylacochrane commented Oct 24, 2024 •
edited
Loading

This PR includes the following updates:

  • Upgrades the Genomic Service Address by updating the container version.

  • Refines the format of reference_cluster.tsv (rclusters) used by GAS CALL to require only id and address columns. This change involved updates to both the append_clusters and cluster_file modules.

  • Updates and modifies associated tests and test data to align with these changes.

Note: Five tests are currently failing due to an adjustment needed in the GAS program: ISSUE12; PR14

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!
  • 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>).
  • CHANGELOG.md is updated.

@github-actions GitHub Actions
Copy link

github-actions bot commented Oct 24, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1a5db26

+| ✅ 144 tests passed       |+
#| ❔  23 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-gasnomenclature_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_light.png
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.max_cpus
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/gasnomenclature/gasnomenclature/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.1
  • Run at 2025-01-08 19:46:27

@kylacochrane kylacochrane changed the base branch from add_profile_databases to dev November 21, 2024 15:25
@kylacochrane
Copy link
Contributor Author

kylacochrane commented Nov 21, 2024 •
edited
Loading

Once a new version of GAS is released, the container directive will need to be updated in the gas/call module. The tests should run as expected and pass CI testing unless there are also changes in the buildNewick function in GAS - see ISSUE15.

In which case, the expected_tree.nwk file in the test/data/clusters file will also need to be updated.

@sgsutcliffe sgsutcliffe self-assigned this Jan 6, 2025
@sgsutcliffe
Copy link
Contributor

Updated the GAS version which fixed the attribute error in the tests but some other errors have poped up:

  • 'Test pipeline with single threshold set to 1'
  • 'Test pipeline with threshold set to 1,0'
  • 'Full pipeline hashes and missing data'
  • 'Full pipeline hashes and missing data count missing as differences'
  • 'Full pipeline remove loci with missing data'

@sgsutcliffe
Copy link
Contributor

sgsutcliffe commented Jan 6, 2025 •
edited
Loading

For 'Test pipeline with single threshold set to 1' and 'Test pipeline with threshold set to 1,0' the address for sampleQ the is 2 and 2.2 respectively. So I updated the called/expected_results* the *_iridanext.output.json files to reflect this. I do this with caution because, based on my understanding the original expected results were correct, and tests are right to fail. 083a678

@sgsutcliffe
Copy link
Contributor

The subsequent tests also had the same issue. Will need to explore as to whether it is the address that was originally wrong or if there is an issue with GAS 0.1.3 26ce6ff

@sgsutcliffe sgsutcliffe marked this pull request as ready for review January 7, 2025 14:18
@sgsutcliffe sgsutcliffe requested a review from apetkau January 7, 2025 14:18
apetkau
apetkau requested changes Jan 7, 2025
View reviewed changes
Copy link
Member

@apetkau apetkau left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks so much Steven. This looks great 😄

And thanks so much @kylacochrane for all your work on this too 😄

I haven't finished reviewing, but sending this PR early since I had one comment.

modules/local/append_clusters/main.nf Outdated Show resolved Hide resolved
This was referenced Jan 8, 2025
Open
Closed
apetkau
apetkau approved these changes Jan 8, 2025
View reviewed changes
Copy link
Member

@apetkau apetkau left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks so much for making that change Steven. Everything else looks great 😄

@sgsutcliffe sgsutcliffe mentioned this pull request Jan 8, 2025
Open
@sgsutcliffe sgsutcliffe merged commit cc6182b into dev Jan 8, 2025
4 checks passed
@sgsutcliffe sgsutcliffe deleted the update_GAS branch January 9, 2025 17:54
@sgsutcliffe sgsutcliffe mentioned this pull request Feb 3, 2025
Open
6 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@sgsutcliffe sgsutcliffe sgsutcliffe left review comments

@apetkau apetkau apetkau approved these changes

Assignees

@sgsutcliffe sgsutcliffe

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@kylacochrane @sgsutcliffe @apetkau