Readme VEP options: remove `--force_overwrite` & add `--fork 4`

huguesrichard / Allopipe

AlloPipe is a computational method to assess the alloreactivity expected from a donor/recipient transplantation pair

MIT License

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Closed PierreLaville closed 4 months ago

PierreLaville commented 4 months ago

it can be confusing to use the --force_overwrite option in VEP by default. Not necessary anymore if the tutorial annotated files are moved in a different directory. And it would be more consistent with this in the readme:

All specified options are mandatory
We could recommend to the user the --fork 4 option:

Using forking enables VEP to run multiple parallel "threads" [...] running VEP with forking enabled can give huge speed increases (3-4x faster in most cases) (source)

adhuyser commented 4 months ago

README.md updated