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- [x] GISAID using their CLI API
- [x] NCBI - BioSample
- [x] NCBI - Genbank
- [x] NCBI - SRA
- [x] NCBI - Table2asn
cc: @leebrian @rchau88 @kristinelacek
nbx0 updated
10 months ago
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Some rows on srarun have a value of zero in the spots column, this is not correct and can be corroborated on the NCBI page for that run.
Example:
(serrauts)
SELECT * FROM srarun WHERE run = 'ER…
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Dear all,
Congratulations on the development of this pipeline, I have had great results.
Would it be possible to download an assembly to enter at the end of the pipeline and perform Antimicrobial Re…
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### Description of the bug
fetchngs successfully handles sra files, but when prefetch gets an sralite file, fasterq-dump can't see it. After fetchngs runs I checked the working directory for the fail…
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Matthew:
Thanks as always!
I think it useful to have the discussion in the Google group (I find I use it quite a lot). So I will follow up here and submit a bug report.
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Version = si…
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https://mp.weixin.qq.com/s/YgWr5yxxcJurmcZ0gkgSBA
ixxmu updated
1 month ago
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I'm trying to bulkload other identifiers that include some new flavors of GenBank identifiers that are not, actually, GenBank but rather different databases at NCBI, such as BioSample (which is in Arc…
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Good morning,
I am willing to re-analyze some data from your publication.
I could download the reads from NCBI SRA, but cannot find in the publication which sample corresponds to OS or OM soil lay…
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### Description of the bug
PRJNA625551 id is not recognised by the pipeline. Perhaps I am using it incorrectly.
### Command used and terminal output
```console
nextflow run nf-core/fetchngs --input…
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Implement validation on accessions that have controlled prefixes.
**BioProject Accession** - Prefix: **PRJNA**
**BioSample Accession** - Prefix: **SAMN**
**SRA** (run) **Accession** - Prefix: **S…