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Implemented TMB score calculation #1738
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 2.14.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Amazing 🌟 Looks like this PR also contains the MSISENSOR changes? @Patricie34 is also implementing variant normalisation over in #1682 , can these efforts be combined/ is that implementation something you can build on? |
Yes somehow msisensorpro tumor-only changes also got into this PR and I cannot separate them. I am not sure if I can help with the variant normalization. |
Hi, are you planning to finish this PR? I am almost done with the normalization and since I will need to calculate TMB in near future, it would be great to have it implemented in Sarek! |
Hi. It's already finished on my end. I am using it on my version of sarek and it works fine. Please feel free to modify it to integrate to the current version of the public version. |
Oh, I see. So you're not planning to resolve the conflicts here so it could be merged? If it works, I could try to finish it here. |
Implements #495 based on pyTMB.py starting from draft by @FriederikeHanssen
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).