Commit 1f5096b6 authored by bow's avatar bow Committed by Peter van 't Hof
Browse files

Use List[_] instead of Option[_] for VEP's --custom flag

As mentioned in the documentation[1], the `--custom` flag can
be specified multiple times.

[1] http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_custom
(cherry picked from commit 5204f4f)
parent 4fc971d4
......@@ -114,7 +114,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var fasta: Option[String] = config("fasta")
var sift: Option[String] = config("sift")
var polyphen: Option[String] = config("polyphen")
var custom: Option[String] = config("custom")
var custom: List[String] = config("custom", default = Nil)
var plugin: List[String] = config("plugin", default = Nil)
var individual: Option[String] = config("individual")
var fields: Option[String] = config("fields")
......@@ -227,7 +227,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
optional("--fasta", fasta) +
optional("--sift", sift) +
optional("--polyphen", polyphen) +
optional("--custom", custom) +
repeat("--custom", custom) +
repeat("--plugin", plugin) +
optional("--individual", individual) +
optional("--fields", fields) +
......
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