Commit 3ce7f8c4 authored by Holger Brandl's avatar Holger Brandl

avoid that _2.fastqs are mapping

parent 49891eaf
......@@ -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() }
......
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