nextflow-io / nextflow-io/nextflow
Cannot invoke method split() on null object with fromSRA
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- Groovy
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Description
Bug report
Expected behavior and actual behavior
No error
Steps to reproduce the problem
cat test_sra.nf
#!/usr/bin/env nextflow
workflow {
// Create a channel using fromSRA with direct accession
Channel
.fromSRA('SRR34839578')
.view()
}
Program output
nextflow run test_sra.nf
N E X T F L O W ~ version 25.04.6
Launching `test_sra.nf` [dreamy_ochoa] DSL2 - revision: fe9803592b
ERROR ~ Cannot invoke method split() on null object
-- Check '.nextflow.log' file for details
Environment
- Nextflow version: 25.04.6
- Docker image: nextflow/nextflow:25.04.6
(error also occurs in a custom install of nextflow)
Additional context
fasterq-dump SRR34839578 works.
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 by running the test_sra.nf reproduction with Channel.fromSRA('SRR34839578') and inspect the resulting .nextflow.log for the null split() call. Trace the fromSRA entry point and verify the direct accession path completes without an error and emits the expected data.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy
- Domain
- data-engineering
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100