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While submitting my project, I created a sdrf.tsv which passed validation:
```bash
% parse_sdrf validate-sdrf --sdrf_file sdrf.tsv
Everything seems to be fine. Well done.
```
But this file wi…
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The [CI currently fails](https://github.com/bigbio/sdrf-pipelines/runs/6774182040?check_suite_focus=true) because some test tries to retrieve
http://purl.obolibrary.org/obo/NCBITaxon_9606&size=100…
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https://mp.weixin.qq.com/s/5wugXfWD4SfN25qGZk4d8Q
ixxmu updated
2 years ago
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Until now, these files only seem accessible when in the same folder and thus one cannot use pkg_resources to access them when being somewhere else.
I suspect that this is due to a missing general s…
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### Description of the bug
```
Pipeline completed with errors-
Error executing process > 'NFCORE_QUANTMS:QUANTMS:DIA:DIANNCONVERT (1)'
Caused by:
Process `NFCORE_QUANTMS:QUANTMS:DIA:DIANNCONV…
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### Description of feature
Dear @daichengxin @vdemichev @jpfeuffer:
I have started testing the DIANN pipeline in quantms. The main problem I found is that still the pipeline is **really slow**.…
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We have an example of one dataset converted in this PR:
https://github.com/bigbio/proteomics-metadata-standard/pull/541
Let us know what you think.
If ok, we can import 204 more datasets fro…
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- [x] I think the source names are not correct in https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD002088/sdrf.tsv
they differ between fractions
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I had some problems with this anndata (the first one in this link: https://developmental.cellatlas.io/fetal-immune#DatasetModalscRNA-seq1). It couldn't get metadata about samples when extracting from …
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Hi @levitsky @pcm32 @foellmelanie @daichengxin @lgatto @anjaf :
We have been developing a simple web app to help the users to autocomplete Ontology terms and PTMs for the SDRF columns (https://ann…