Commit 6b5fcd52 authored by Holger Brandl's avatar Holger Brandl

rewritten scala utils in kotlin

parent def09006
......@@ -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""")
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