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Disable/enable variant callers through CLI #411

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hassanfa opened this issue Sep 9, 2020 · 0 comments · Fixed by #417
Closed

Disable/enable variant callers through CLI #411

hassanfa opened this issue Sep 9, 2020 · 0 comments · Fixed by #417

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@hassanfa
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hassanfa commented Sep 9, 2020

Is your feature request related to a problem? Please describe.
Occasionally some variant callers fail due to timeouts, bug, or stall for hard to call regions. There should be an option to enable or disable them.

Describe the solution you'd like
Disable or enable variant callers through CLI

Describe alternatives you've considered
Modular workflows, but it won't make it possible to disable/enable at will.

Additional context
Mutect2 is notorious for timeout and long computation time. It is useful to disable it occasionally.

Expected output for the feature
balsamic run analysis .... --disable-var-caller mutect2

Current BALSAMIC version
5.1.0

@hassanfa hassanfa linked a pull request Sep 21, 2020 that will close this issue
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