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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
+5 −3

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grst
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@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
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github-actions bot commented Mar 21, 2024 •
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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
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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
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