fixed madmax config

dge_workflow/star_align.kts

@@ -8,7 +8,6 @@
 
 import joblist.JobConfiguration
 import joblist.JobList
-import joblist.ResubmitStrategy
 import kutils.evalBash
 import org.docopt.Docopt
 import java.io.File
@@ -76,7 +75,7 @@ fastqFiles.filter { !it.isFile }.let {
 
 println("Running STAR using igenome '${igenome}' for the following files:\n ${fastqFiles.joinToString("\n")}")
 
-val jl = JobList(".starjobs")
+val jl = JobList(".starjobs").apply { reset() }
 
 for (fastqFile in fastqFiles) {
     println("submitting STAR job for $fastqFile")
@@ -101,7 +100,7 @@ for (fastqFile in fastqFiles) {
     // or use process substiutation in case of zipped reads (see https://github.com/alexdobin/STAR/issues/143#issuecomment-216597465)
 
     // detect if paired end reads are supplied
-    val revReads = if (isPE) fastqFile.parentFile.resolve(fastqFile.name.replace("_1.fastq", "_2.fastq")).path else ""
+    val revReads = if (isPE) fastqFile.absoluteFile.parentFile.resolve(fastqFile.name.replace("_1.fastq", "_2.fastq")).path else ""
 
     val cmd = """
     STAR --genomeDir ${star_index} --readFilesIn ${fastqFile} ${revReads} --runThreadN 6 ${optionalZcat} --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs   RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3
@@ -113,7 +112,8 @@ for (fastqFile in fastqFiles) {
     // todo provide proper walltime here
     // slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/
     // sacct -o MaxRSS -j JOBID
-    jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "10:00", "", 5, 40000, "", better.files.File(File(".").toPath())))
+//    jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "10:00", "", 5, 40000, "", better.files.File(File(".").toPath())))
+    jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "", "medium", 5, 0, "", better.files.File(File(".").toPath())))
 }