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Fix pipeline specific options in docs
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nvnieuwk committed Apr 9, 2024
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Expand Up @@ -83,7 +83,7 @@ Less common options for the pipeline, typically set in a config file.
Options specific to the execution of this pipeline

| Parameter | Description | Type | Default | Required | Hidden |
| --------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ----------------------------------------------------------------------------------------------------------------------------------- | -------- | ---------------------------------------------- | --- | --- |
| --------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ----------------------------------------------------------------------------------------------------------------------------------- |
| `callers` | A comma-seperated list of callers to use. Can be one or more these: smoove | delly | manta | gridss | expansionhunter. At the moment Gridss runs very slowly compared to all other tools so it's only advised to use it when it's needed. | `string` | manta,smoove,delly,expansionhunter,wisecondorx | | |
| `output_callers` | Output the VCF files from different callers. Warning: This produces a lot of additional output and should only be used for testing purposes | `boolean` | | | |
| `sv_callers_support` | The minimum amount of SV callers that should detect a variant. All variants that have a lower amount of callers supporting it, will be removed. (Only used when more than one caller is given) | `integer` | 1 | | |
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