Merge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_tools

.gitignore

 # Created by .gitignore support plugin (hsz.mobi)
 .idea
+*.iml

dge_workflow/star_align.kts

@@ -73,6 +73,11 @@ fastqFiles.filter { !it.isFile }.let {
     require(it.isEmpty()) { "Some fastq files do not exist  ${it.map { it.absoluteFile }.joinToString(", ")}" }
 }
 
+require(fastqFiles.filter { it.name.contains("_2.fastq") }.isEmpty()){
+    """Mapping 2nd mate alone is unlikely to have meaningful semantics.
+     Just provide _1 and star_align.kts will pick up corresponding _2 for PE alignment if present"""
+}
+
 println("Running STAR using igenome '${igenome}' for the following files:\n ${fastqFiles.joinToString("\n")}")
 
 val jl = JobList(".starjobs").apply { reset() }