From 3124a44badcae5e1099dc72c32e9c7f3d283120a Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Thu, 8 Feb 2024 15:06:29 -0800 Subject: [PATCH] Add file to command line parser --- .../scala/org/broadinstitute/gpp/poolq3/PoolQConfig.scala | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/main/scala/org/broadinstitute/gpp/poolq3/PoolQConfig.scala b/src/main/scala/org/broadinstitute/gpp/poolq3/PoolQConfig.scala index e3491ac..b32ec39 100644 --- a/src/main/scala/org/broadinstitute/gpp/poolq3/PoolQConfig.scala +++ b/src/main/scala/org/broadinstitute/gpp/poolq3/PoolQConfig.scala @@ -254,6 +254,11 @@ object PoolQConfig { val _ = opt[Path]("quality").valueName("").action((f, c) => c.copy(output = c.output.copy(qualityFile = f))) + val _ = + opt[Path]("condition-barcode-counts-summary") + .valueName("") + .action((f, c) => c.copy(output = c.output.copy(conditionBarcodeCountsSummaryFile = f))) + val _ = opt[Path]("counts").valueName("").action((f, c) => c.copy(output = c.output.copy(countsFile = f))) val _ = opt[Path]("normalized-counts").valueName("").action { (f, c) =>