Schema validation blocks multiple BAMs per sample
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bug
- Dominant language
- Nextflow
- Stars
- 3
- Forks
- 5
- PR merge metrics
- No merged PRs in 30d
Description
Description of the bug
You cannot have more than one BAM file per sample because the schema validation blocks it.
Command used and terminal output
Crashes with
ERROR ~ Validation of pipeline parameters failed!
-- Check '.nextflow.log' file for details
The following invalid input values have been detected:
* --input (./samplesheet.csv): Validation of file failed:
-> Entry 2: Detected duplicate entries: [patient:PAT001, sample:PAT001-T1]
Relevant files
Can be fixed with
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 2144d79..603248d 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -4,7 +4,6 @@
"title": "nf-core/pacsomatic pipeline - params.input schema",
"description": "Schema for the file provided with params.input",
"type": "array",
- "uniqueEntries": ["sample", "patient"],
"items": {
"type": "object",
"properties": {
System information
No response
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 assets/schema_input.json and inspect the uniqueEntries setting that rejects duplicate patient and sample entries. Remove the restriction so a samplesheet can contain multiple BAM files for one sample, then confirm pipeline parameter validation accepts the reported input.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- json
- Domain
- data
- Issue type
- Bug
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 35/100