nextflow-io / nextflow-io/nextflow
'Unable to download path' on Azure when data in separate container from work
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- Dominant language
- Groovy
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Description
Bug report
This seems to be the same problem as issue #2563, but I am encountering it in 24.11.0-edge build 5929. Copying data over to the same container as work / output folder resolved the problem.
Expected behavior and actual behavior
- nextflow should be able to stage data from separate container
- it can't
Steps to reproduce the problem
Working on this, will update issue when I have it ready.
Program output
From .command.log in work dir:
Unable to download path: https://omicsdata.blob.core.windows.net/study-data/{stuff}.fastq.gz
Unable to download path: https://omicsdata.blob.core.windows.net/study-data/{stuff}.fastq.gz
Environment
- Nextflow version: 24.11.0-edge build 5929
- Java version: [?]
- Operating system: Linux
- Bash version: (use the command
$SHELL --version)
Additional context
(Add any other context about the problem here)
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 the .command.log output and the Azure Blob URL shown in the report, then compare this failure with issue #2563. Reproduce staging data from a separate container using Nextflow 24.11.0-edge build 5929; the issue is complete when that data stages successfully without copying it into the work or output container.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- azure, groovy
- Domain
- cloud
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100