Commit b32e2aa7 authored by Holger Brandl's avatar Holger Brandl

improved bash wrapper

parent ad70d502
......@@ -28,18 +28,21 @@ Options:
val doArgs = Docopt(usage).parse(args.toList()).map {
it.key.removePrefix("--").replace("[<>]", "") to it.value?.toString()
it.key.removePrefix("--").replace("[<>]".toRegex(), "") to it.value?.toString()
// extract all configuration parameters
val fastqFiles = (doArgs["fastq_files"] as String).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")
println("validating inputs...")
// make sure that STAR is in the PATH
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