From 7b2cc543c41a5cd6465f79aa9707d9832fbf96cd Mon Sep 17 00:00:00 2001
From: hpratt <hpratt111@live.com>
Date: Sun, 24 May 2020 20:13:20 -0400
Subject: [PATCH] add index prefix tar parameter for RSEM

---
 workflow/build.gradle.kts                           | 2 +-
 workflow/src/main/kotlin/workflow/task/Rsemquant.kt | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/workflow/build.gradle.kts b/workflow/build.gradle.kts
index 4361a42..cdd16e4 100644
--- a/workflow/build.gradle.kts
+++ b/workflow/build.gradle.kts
@@ -9,7 +9,7 @@ plugins {
 }
 
 group = "com.genomealmanac.rnaseq"
-version = "1.1.4"
+version = "1.1.5"
 val artifactID = "rnaseq-workflow"
 
 repositories {
diff --git a/workflow/src/main/kotlin/workflow/task/Rsemquant.kt b/workflow/src/main/kotlin/workflow/task/Rsemquant.kt
index 09dcdb2..09093eb 100644
--- a/workflow/src/main/kotlin/workflow/task/Rsemquant.kt
+++ b/workflow/src/main/kotlin/workflow/task/Rsemquant.kt
@@ -12,7 +12,8 @@ data class RsemQuantParams(
     val strand: String = "unstranded",
     val seed: Int? = null,
     val cores: Int = 1,
-    val ramGb: Int = 16
+    val ramGb: Int = 16,
+    val indexTarPrefix: String? = null
 )
 
 data class RsemQuantInput(
@@ -50,6 +51,7 @@ fun WorkflowBuilder.rsemquantTask(name: String, i: Publisher< RsemQuantInput>)
                 --strand ${params.strand} \
                 --cores ${params.cores} \
                 --ram-gb ${params.ramGb} \
+                ${ if (params.indexTarPrefix !== null) "--index-tar-prefix ${params.indexTarPrefix}" else "" } \
                 ${ if (params.seed !== null) "--seed ${params.seed}" else "" } \
                 ${ if (input.pairedEnd) "--paired-end" else "" }
     """