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Published 20 hours ago • verified publisher icon nf-core

Can SRA responses be trapped and reported in a user-friendly manner?

Open telatin opened this issue 1 year ago • 1 comments

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

telatin avatar Jul 14 '22 10:07 telatin