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Lots of people use nf-core pipelines offline. We want to make the process of using modules from a different repository as simple as possible.
One solution would be to use `git submodule` to add `nf…
ewels updated
4 years ago
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We should do this with some due diligence to make sure we're not throwing important stuff away:
Barry wrote
"""
Deleting from current output that are not mentioned above:
• somatic_variants/de…
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Below two lines result in duplicated level of neoantigen directory in the "Result" folder when publishing the result
https://github.com/mskcc/vaporware/blob/bfc446dc16336802790e6644f37e1e9f0cc32fd8…
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The default non-logged view is not helpful for Immune Feature Trends violin plots for variables such as mutation rates and neoantigen counts
![image](https://user-images.githubusercontent.com/28378…
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The Dockerfile here obviously isn't a long term solution (and actually don't make sense for reproducibility)
```
FROM biocontainers/biocontainers:latest
LABEL base.image="biocontainers:latest"
…
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The latest VEP release is 96 (http://grch37.ensembl.org/info/docs/tools/vep/script/vep_download.html#new). However, the `neoantigen.py` script in https://github.com/taylor-lab/neoantigen-dev does curr…
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Hi Sebastian,
Was wondering if before the new major release is out, is it easy enough/straightforward to "just" add the transcript IDs in the output of arriba? This is an essential piece of informa…
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Hello all,
I read your paper today and I am interesting with your pipeline. But I find netMHCpan, but no netMHCIIpan. Does it mean that we can't deal with the HLA class II data using the Pipeline? I…
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Adding modules to the Snakefile
- [x] OptiType
- [x] pvacseq
- [x] Sequenza (?)