accommodate ENCODE TAR files with internal names differing from the TAR name

Author: hpratt

build.gradle.kts

@@ -8,7 +8,7 @@ plugins {
 }
 
 group = "com.genomealmanac.rnaseq"
-version = "1.0.5"
+version = "1.0.6"
 val artifactID = "rsem"
 
 repositories {

src/main/kotlin/App.kt

@@ -27,6 +27,7 @@ class Cli : CliktCommand() {
     private val cores: Int by option("--cores", help = "number of cores available to the task").int().default(1)
     private val ram: Int by option("--ram-gb", help = "amount of RAM available to the task, in GB").int().default(16)
     private val indexTarPrefix: String? by option("--index-tar-prefix", help = "the root directory of files in the index tar archive")
+    private val indexNamePrefix: String? by option("--index-name-prefix", help = "prefix of the name of the files in the index tar archive")
 
     override fun run() {
         DefaultCmdRunner().runRSEMQuant(
@@ -40,7 +41,8 @@ class Cli : CliktCommand() {
                 outputDirectory = outputDirectory,
                 cores = cores,
                 ram = ram,
-		indexTarPrefix = indexTarPrefix
+		indexTarPrefix = indexTarPrefix,
+		indexNamePrefix = indexNamePrefix
             )
         )
     }

src/main/kotlin/step/rsemquant.kt

@@ -17,7 +17,8 @@ data class RSEMParameters (
     val ram: Int = 16,
     val outputPrefix: String = "output",
     val pairedEnd: Boolean,
-    val indexTarPrefix: String? = null
+    val indexTarPrefix: String? = null,
+    val indexNamePrefix: String? = null
 )
 
 val FORWARD_PROB: Map<String, Float> = mapOf(
@@ -31,6 +32,7 @@ fun CmdRunner.runRSEMQuant(parameters: RSEMParameters)  {
     // create output directory, unpack index
     this.run("tar xvf ${parameters.index} -C ${parameters.outputDirectory}")
     if (parameters.indexTarPrefix !== null) this.run("mv ${parameters.outputDirectory}/${parameters.indexTarPrefix}/* ${parameters.outputDirectory}")
+    val indexNamePrefix = if (parameters.indexNamePrefix !== null) parameters.indexNamePrefix else parameters.index.getFileName().toString().split(".tar.gz")[0]
 
     // run RSEM
     this.run("""
@@ -45,7 +47,7 @@ fun CmdRunner.runRSEMQuant(parameters: RSEMParameters)  {
             --forward-prob ${FORWARD_PROB[parameters.strand]} \
             ${ if (parameters.pairedEnd) "--paired-end" else "" } \
             ${parameters.bam} \
-            ${parameters.outputDirectory.resolve(parameters.index.getFileName().toString().split(".tar.gz")[0])} \
+            ${parameters.outputDirectory.resolve(indexNamePrefix)} \
             ${parameters.outputDirectory.resolve("${parameters.outputPrefix}")}
     """)