Test config - panel field does not contains a valid key!
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bug
- Dominant language
- Nextflow
- Stars
- 15
- Forks
- 11
- Avg merge
- 1d 17h
- Merged PRs (30d)
- 11
Description
Description of the bug
When running the pipeline with the test data from the test-dataset and configuration of the test.config the following error occurs:
Container:
quay.io/pixelgen-technologies/pixelator:0.22.1
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Dec-04 07:08:38.642 [Actor Thread 15] ERROR nextflow.Nextflow - Please check input samplesheet -> panel field does not contains a valid key!
Input: human-sc-immunology-spatial-proteomics
Valid options:
-
### Command used and terminal output
```console
nextflow run 'https://github.com/nf-core/pixelator' -hub github -with-report 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/report.html' -with-timeline 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/timeline.html' -with-dag 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/dag.html' -with-trace 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/trace.tsv' -c nextflow-s3.config -c tower.config -c /vol/projects/clowm/nextflow.config -revision 1affbf6a29e608424038d17baf69cac37e2fa477 -params-file params.json
Relevant files
nextflow-debug-019ae82fc5697a989a9af30d3f7f8ab7.log
System information
Nextflow version: 25.10.0
Executor: slurm
Container engine: Docker
Version of nf-core/pixelator: 2.2.0
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the test-dataset and test.config, then reproduce the failure from the process work directory by running bash .command.run. Trace why the samplesheet panel value has no valid options; done means the test configuration accepts human-sc-immunology-spatial-proteomics without the reported validation error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker
- Domain
- devops, testing
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 38/100