fixed incorrect wall time

dge_workflow/dge_star_template.sh

@@ -49,9 +49,9 @@ dge_fastqc $(ls *fastq.gz) &
 mcdir $baseDir/lanereps_pooled
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/core_commons.R")
 
-options(java.parameters = "-Xmx4g" ); library(xlsx)
+options(java.parameters = "-Xmx4g" ); require_auto(xlsx)
 
 sheetFile <- "../originals/natalied-FC_SN678_338-2015-5-12.xls"
 

dge_workflow/star_align.kts

@@ -37,7 +37,7 @@ val doArgs = Docopt(usage).parse(args.toList()).map {
 //doArgs["fastq_files"]
 
 // extract all configuration parameters
-val fastqFiles = (doArgs["fastq_files"] as String).substring(1).substringBefore("]").split(" ").map { File(it) }
+val fastqFiles = (doArgs["fastq_files"] as String).substring(1).substringBefore("]").split(", ").map { File(it) }
 val igenome = File(doArgs["igenome"])
 val star_index = File(igenome, "Sequence/StarIndex")
 val gtfFile = if (doArgs["gtfFile"] != null) File(doArgs["gtfFile"]) else File(igenome, "Annotation/Genes/genes.gtf")
@@ -65,7 +65,9 @@ if (!File("${star_index}/SA").isFile())
 //   dge_create_star_index ${igenome}'
 
 
-// make sure all fastq files do exist
+//println("files are ${fastqFiles.joinToString(", ")}")
+// make sure all fastq files do exist (for symlinks see http://www.java2s.com/Code/Java/JDK-7/Isfileasymboliclink.htm
+//fastqFiles.filter { !(it.exists()  || Files.isSymbolicLink(it.toPath())) }.let {
 fastqFiles.filter { !it.isFile }.let {
     require(it.isEmpty()) { "Some fastq files do not exist  ${it.map { it.absoluteFile }.joinToString(", ")}" }
 }
@@ -95,7 +97,7 @@ for (fastqFile in fastqFiles) {
     samtools index ${fastqBaseName}.bam
     """.trimIndent()
 
-    jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", null, "medium", 5, "", better.files.File(File(".").toPath())))
+    jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "", "medium", 5, "", better.files.File(File(".").toPath())))
 }