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I think the ENA scraper might be broken. https://circleci.com/gh/AlexsLemonade/refinebio/15332
```
WARNING:data_refinery_foreman.surveyor.harmony:Cannot determine sample title!
2019-03-25 18:06:5…
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As requested by @lshep: currently, `bfcrpath` prints out a progress bar, which is nice in interactive sessions but annoying when compiling Rmarkdown documents. Ideally this could be turned off - or ev…
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### Context
Jackiecrunch (#466)
### Problem or idea
We are performing some smoothing of the sample metadata and these harmonized values are the ones being displayed in the samples table view.…
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Samples on ArrayExpress have meta-information in `sdrf` files. We may want to turn some of this information into structured/harmonized fields on our sample table, and to define some harmony with sampl…
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I'm adding that expression atlas downloader now (#489), and wondering where the files should go.
`pbmc68k_reduced` and `toggleswitch` put the datasets relative to where scanpy is installed (via `__…
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### Context
Once https://github.com/AlexsLemonade/refinebio/pull/447 lands, we should be able to do the following identifier conversions for submitter-processed data:
* Illumina BeadArray: Probe…
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To keep the prototype I'm building is consistent with the data available/extractable in the back end, here are the experiment fields(unordered):
- Abstract
- Publication and link to publication
- S…
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I have a PR coming for the reheadering which will fix the vcf reheadering. I am however getting this error:
```
[varscan.snp.genome.wustl.edu.TCGA-W5-AA33.vcf] VCF header validation error: SAMPLE hea…
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I’m using clustermq to download large files via the R function `utils::download.files`. Unfortunately, that function reports presumably failed downloads as a warning. As this warning isn’t propagated …
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`magetab2isatab` splitting of table sometimes outputs empty cells, noticed on test `test_get_experiment_as_isatab_afmx_2()` that splits the E-AFMX-2 SDRF file.
Possible a problem with reading the S…