A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I am going to tackle this one next <https://github.com/nf-core/sarek/issues/1861|github.com/nf-core/sarek/issues/1861> : MSI tool for tumor/normal calling that ideally doesn't have a restrictive commercial license. if anyone has a tool preference let me know.

We recently forked MSIsensor PRO, free for non commercial use
<https://github.com/CenterForMedicalGeneticsGhent/msisensor-pro|github.com/CenterForMedicalGeneticsGhent/msisensor-pro>

this issue is asking for one for commercial use: <https://github.com/nf-core/sarek/issues/1861|github.com/nf-core/sarek/issues/1861> we have msisensor-pro already in the pipeline :slightly_smiling_face:

why did you fork it? Wondering if we should switch to your

We needed a feature and they didn’t seem very responsive, so we forked it and made a release of our own

The current version counts duplicate reads twice, our version has a flag to ignore duplicates

We also submitted a PR with our changes on the off chance it get merged

Oh yeah, I also ditched the ancient HTSlib that was vendored in and replaced it with a git submodule that’s easier to update

And the CI now builds the artefacts and adds them to the release, so no more compiled binaries in the repo