nf-core / nf-core/pacsomatic

Schema validation blocks multiple BAMs per sample

Open
#3 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

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

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 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.