aws-samples / aws-samples/aws-healthomics-tutorials

scrnaseq.nf failure with engine error 'NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC'

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Dominant language
Python
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Forks
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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

Open the contributing 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

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