Can SRA responses be trapped and reported in a user-friendly manner?
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 202
- Forks
- 93
- Avg merge
- 1d 18m
- Merged PRs (30d)
- 15
Description
Description of feature
Running:
nextflow run nf-core/fetchngs -r 1.7 --input list.txt --outdir sra -profile docker
Pipeline fails at NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO:
[ERROR] The server couldn't fulfill the request.
[ERROR] Status: 429 Too Many Requests
as the error is buried in the failed task report, it can be a bit intimidating so I was wondering if this kind of problems can be trapped and reported from the workflow itself (e.g. messages from the pipeline like parameter validation)
- nextflow 21.10.6 build 5660
- Cloud VM (OpenStack)
- Executor: local
- OS: "Ubuntu 20.04.3 LTS"
- Container: Docker
- fetchngs 1.7
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 NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO process and reproduce the 429 failure using the command and inputs in the report. Determine how the workflow currently surfaces SRA request errors; done means rate-limit failures are reported through a clear user-facing workflow message rather than only in the failed task report.
Written by the indexing model from the issue text.
Assessment
- Domain
- data-engineering
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100