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

Refactor FILTER_QUERY to Handle Query Sample IDs via File Input for csvtk #24

Merged
merged 4 commits into from
Sep 13, 2024
Merged

Refactor FILTER_QUERY to Handle Query Sample IDs via File Input for csvtk #24

merged 4 commits into from
Sep 13, 2024

Conversation

kylacochrane
Copy link
Contributor

@kylacochrane kylacochrane commented Sep 11, 2024 •
edited
Loading

The FILTER_QUERY module has been refactored to improve how query sample IDs are handled. Instead of passing sample IDs as individual strings to csvtk filter2, the IDs are now written to a single file (.collectFile) in the workflow and passed directly into csvtk grep.

This change prevents errors caused by overly long command-line strings and simplifies the process of handling large numbers of query samples efficiently.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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 Sep 11, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 72dff81

+| ✅ 145 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.2.2
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/gasnomenclature/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/nextflow_schema.json

❔ 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
  • 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 2.14.1
  • Run at 2024-09-12 20:42:22

@kylacochrane kylacochrane marked this pull request as ready for review September 12, 2024 20:50
emarinier
emarinier approved these changes Sep 13, 2024
View reviewed changes
Copy link
Member

@emarinier emarinier left a comment

Choose a reason for hiding this comment

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

Looks good to me.

@sgsutcliffe
Copy link
Contributor

Looks good! Hadn't really looked into the documentation of csvtk before (except that one time I used it in staramr). Looks handy! Good to keep in mind instead of doing everything in bash code blocks!

apetkau
apetkau approved these changes Sep 13, 2024
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.

This is great work @kylacochrane . I'm glad it was such a small change too 😄

@kylacochrane kylacochrane merged commit c924f2d into dev Sep 13, 2024
4 checks passed
@kylacochrane kylacochrane deleted the update_filterquery branch September 20, 2024 14:33
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@apetkau apetkau apetkau approved these changes

@emarinier emarinier emarinier approved these changes

@sgsutcliffe sgsutcliffe sgsutcliffe approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

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