add index prefix tar parameter for RSEM

weng-lab · May 25, 2020 · 7b2cc54 · 7b2cc54
1 parent 35db323
commit 7b2cc54
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git 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
@@ -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 "" }
     """