Comments (4)
Yeah, fair point. I would put this as another pointer towards using ffq #110 If you have the time and it's important to you right now, introducing ffq should be quite straight forward.
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thanks @Midnighter - looks like @drpatelh is on top of it already (#100)! I haven't looked closely at that but I'll just add that I'd guess that simply swapping in calls to ffq to the current parallel structure would likely end up hitting the same rate limit issue ( see https://github.com/pachterlab/ffq#failure-modes number 4). So probably trying to use batching for the metadata calls would be relevant in any case?
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Still haven't had time to look into adding ffq
properly I'm afraid 😏 Going to get a maintenance release out in the next couple of days. We can maybe assess this after we have added ffq
support.
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Btw, the only way to avoid this is by calling the run info resolution in a single process that can control the request rate. As soon as multiple processes are started in parallel, all bets are off.
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Related Issues (20)
- TypeError: unsupported operand type(s) for |: 'dict' and 'dict' HOT 1
- error executing process HOT 3
- Add compatibility with sarek samplesheet
- SRAtools download seems to insert paired-end suffix into workdir path HOT 6
- Support .ngc file for dbgap downloads HOT 2
- FEAT: Pass scientific name as input to download the data
- Pipeline fails for large studies HOT 1
- Pipeline crashes if some samples are not available HOT 3
- Use nf-test for input validation
- check out extensions for input files HOT 1
- Add ability to download more than 2 FastQ files via FTP and Aspera HOT 3
- Merge technical replicates (SRR1 + SRR2 -> SRX)
- nf-validation-1.1.3: Operation not supported HOT 20
- `vdb-validate` does not detect file corruption HOT 5
- URGENT: pin nf-validation version HOT 1
- wget host address error HOT 5
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