rewritten scala utils in kotlin

dge_workflow/star_align.kts

@@ -7,7 +7,7 @@
 
 import joblist.JobConfiguration
 import joblist.JobList
-import kutils.bashEval
+import kutils.evalBash
 import org.docopt.Docopt
 import java.io.File
 
@@ -46,7 +46,7 @@ println("validating inputs...")
 
 
 // make sure that STAR is in the PATH
-if (bashEval("which STAR").exitCode != 0) throw IllegalArgumentException("STAR aligner is not in PATH")
+if (evalBash("which STAR").exitCode != 0) throw IllegalArgumentException("STAR aligner is not in PATH")
 
 
 // check if gtf file exists
@@ -110,13 +110,13 @@ joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport()
 
 
 // cleanup
-bashEval("""rm - rf * STARgenome * .Log.progress.out _STARtmp * .SJ.out.tab *Log.out""")
+evalBash("""rm - rf * STARgenome * .Log.progress.out _STARtmp * .SJ.out.tab *Log.out""")
 
 // Test for bam correlation (but don't wait for the results)
-bashEval("""
+evalBash("""
 rend.R - e ${ System.getenv("NGS_TOOLS") } / dge_workflow / star_qc.R.
 dge_bam_correlate &
 """)
 
 // Condense counts into matrix
-bashEval("""dge_star_counts2matrix""")
+evalBash("""dge_star_countas2matrix""")