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Now that we've reconfigured and refactored the phasing pipeline to improve SV performance on 10Mbp, we probably need to make additional changes to improve scalability for whole chromosome/genome runs.…
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Is there a way to specify the -r option per read? My samples are a mix of pacbio and nanopore reads. I was guessing the SV and SNP genotyping would be more accurate if I called on the whole population…
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Now that we are providing automatic package upgrades, it would be helpful for us to be able to verify that an upgrade successfully landed on every known SecureDrop instance. We can sort of do this for…
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Hi,
I would really like to use quip to view and analyze til classification heatmaps but I’m struggling with the setup.
Would it be possible to get more information about what to do at step 4 “Config…
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Hey there!
Thanks so much for this project, overall has been a joy to work with.
One little hangup we're having is including "openslide.dylib"-type files. I've tried the following with _some_ su…
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## Description
There should be one run script that we can use on sd-app, sd-dev, and outside of Qubes. Right now we have to run `python -m securedrop_client` in sd-app, which could easily be added …
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I have installed pyvips using pip on python 3.7.7 virtual environment. When I try to load an svs image at {{PATH_TO_FILE}} I get:
```
Python 3.7.7 (default, Mar 23 2020, 17:31:31)
[Clang 4.0.1 (t…
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When I come to the website, it says: “All slide and diagnostic images from the TCGA program are currently unavailable for download”. Could you share the lung datasets by using a Google Cloud link? : )…
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I am converting SVS files (~500+MB each) to OME-zarr. My command line looks like this:
`${params.cmd} --max_workers=${params.max_workers} --compression=zlib --compression-properties level=9 --resolu…
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Flask has been giving me too many headaches lately, and I've been wanting to learn/use FastAPI.
I'm going to rewrite the internals of `localtileserver` to strip out flask and use fastapi. The avera…