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

Fix schema validation for spaceranger reference #73

Merged
merged 3 commits into from
Apr 12, 2024
Merged

Fix schema validation for spaceranger reference #73

merged 3 commits into from
Apr 12, 2024

Conversation

grst
Copy link
Member

@grst grst commented Mar 21, 2024

Needs to be path instead of file-path because it can be either directory or file.

Before it failed for me with

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --spaceranger_reference: '/<redacted>/refdata-gex-GRCh38-2020-A' is not a file, but a directory (<redacted>/refdata-gex-GRCh38-2020-A)`

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/spatialtranscriptomics 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).

@grst
Fix schema validation for spaceranger reference
e2c05d1 
Needs to be `path` instead of `file-path` because it can be either directory or file. 

Before it failed for me with

```
ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --spaceranger_reference: '/<redacted>/refdata-gex-GRCh38-2020-A' is not a file, but a directory (<redacted>/refdata-gex-GRCh38-2020-A)`
```
@github-actions GitHub Actions
Copy link

github-actions bot commented Mar 21, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2338ae9

+| ✅ 171 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialtranscriptomics_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialtranscriptomics_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialtranscriptomics_logo_dark.png
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-12 12:34:32

@fasterius
Copy link
Collaborator

Looks good to me! Not sure if we should ignore the failing CI stuff and force-merge this right now or not, since a lot of stuff is broken while waiting for #67 regardless.

@fasterius fasterius merged commit b882ba4 into dev Apr 12, 2024
5 of 6 checks passed
@fasterius fasterius deleted the grst-patch-1 branch April 12, 2024 12:46
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@fasterius fasterius fasterius 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.
2 participants
@grst @fasterius