Updated get_manta_sv doesn't work for remote users

morinlab / GAMBLR

Set of standardized functions to operate with genomic data

https://morinlab.github.io/GAMBLR/

MIT License

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Updated get_manta_sv doesn't work for remote users #226

Open rdmorin opened 1 year ago

rdmorin commented 1 year ago

This issue is caused by a new path for the manta merges. These new merges need to be synced by the accompanying snakefile in order to fix this.

> all_svs = get_manta_sv()
[1] "missing:  /Users/rmorin/gambl_results/gambl/manta-2.3/merges/manta.genome--grch37.bedpe"
Error: '/Users/rmorin/gambl_results/gambl/manta-2.3/merges/manta.genome--grch37.bedpe' does not exist.

mattssca commented 6 months ago

Kostia will close this once he has pushed the updated snakefile from my closed branch.