nf-core / nf-core/pixelator

Test config - panel field does not contains a valid key!

Open
#167 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.