aws-samples / aws-samples/aws-healthomics-tutorials
scrnaseq.nf failure with engine error 'NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC'
- Dominant language
- Python
- Stars
- 94
- Forks
- 42
- PR merge metrics
- No merged PRs in 30d
Description
run failed after completing mtx_conversion and while starting multiqc with the following engine error:
Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC'
Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
for example data from HealthOmics R2R workflow.
Deleting Line 214 in scrnaseq.nf did work.
https://github.com/aws-samples/amazon-omics-tutorials/blob/main/example-workflows/nf-core/workflows/scrnaseq/workflows/scrnaseq.nf#L214
Contributor guide
Research direction
Open workflows/scrnaseq/scrnaseq.nf and inspect line 214, then compare it with the linked nf-core workflow and the HealthOmics R2R example context. Reproduce the MULTIQC startup failure and confirm that the workflow completes without the null path error while retaining the mtx_conversion output.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- aws
- Domain
- cloud, data-engineering
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100