Sailfish paired end

public/scala/src/org/broadinstitute/sting/queue/extensions/yeo_scripts/yeo/STAR.scala

@@ -42,7 +42,7 @@ class STAR extends CommandLineFunction {
   var alpha: Boolean = false
 
   this.wallTime = Option((8 * 60 * 60).toLong)  
-  this.nCoresRequest = Option(8) 
+  this.nCoresRequest = Option(16) 
   var gzip_regex = ".gz$".r
 
   override def shortDescription = "STAR"  

public/scala/src/org/broadinstitute/sting/queue/extensions/yeo_scripts/yeo/Sailfish.scala

@@ -7,9 +7,12 @@ import org.broadinstitute.sting.queue.function.CommandLineFunction
 class Sailfish extends CommandLineFunction {
 
 
-  @Input(doc="input fastq file", shortName = "inFastq", fullName = "input_fastq_file", required = true) 
+  @Input(doc="input fastq file, read1", shortName = "inFastq", fullName = "input_fastq_file", required = true) 
   var inFastq: File = _
 
+  @Input(doc="input fastq file, read 2", shortName = "inFastqPair", fullName = "input_fastq_file", required = false) 
+  var inFastqPair: File = _
+
   @Output(doc="output dir file", shortName = "outDir", fullName = "out_dir_file", required = true) 
   var outDir: File = _
 
@@ -18,18 +21,26 @@ class Sailfish extends CommandLineFunction {
 
   @Argument(doc="sh script to output", shortName = "shScript", fullName = "ash_script", required = false)
   var shScript: String = _
+
+  @Argument(doc="If provided, then the reads are strand-specific. Otherwise, the reads are assumed to be unstranded.", 
+    shortName = "stranded", fullName = "strand_specific", required = false)
+  var stranded: Boolean = false
 
   override def shortDescription = "sailfish"
   this.nCoresRequest = Option(16)
+
+  this.wallTime = Option((4 * 60 * 60).toLong) 
 
   def commandLine = "sailfish_quant.py" +
   required("-1", inFastq) +
+  optional("-2", inFastqPair) +
+  conditional(stranded, "--stranded") +
   required("--out-dir", outDir) +
   required("--index", index) +
   required("-n", shScript) +
   required("--out-sh", shScript) +
   required("-i", index) +
-  "-p 16 --do-not-submit && echo $(tail -n 2 " +
+  "-p 16 --not-gzipped --do-not-submit && echo $(tail -n 2 " +
   required(shScript) +
   ") | bash"            
 }

public/scala/src/org/broadinstitute/sting/queue/util/TsccUtils.scala

@@ -37,6 +37,18 @@ object TsccUtils {
    retval
   }
 
+  def sailfishGenomeIndexLocation(genome: String) : String = {
+   //returns sailfish location for TSCC
+     var retval = "none"
+     if (genome == "hg19") {
+       retval = genome_directory + "/hg19/sailfish/gencode.v19.pc_lncRNA_transcripts.ercc_fluidigm_spikein.fa_sailfish_index_k31"
+     }else if(genome == "mm10") {
+       retval = genome_directory + "/mm10/sailfish_fixed/gencode.vM2.pc_lncRNA_transcripts.ercc_fluidigm_spikein.gfp.fa_sailfish_index"
+     }
+     retval
+  }
+
+
   def chromSizeLocation(genome: String) : String = {
   //Returns star genome Location for TSCC, could eventually be factored out into conf file