Commit d35a71dd authored by Holger Brandl's avatar Holger Brandl

updated dependencies

parent 72893bc8
#!/usr/bin/env kscript
//DEPS de.mpicbg.scicomp:joblist:0.6 de.mpicbg.scicomp:kutils:0.2-SNAPSHOT
//DEPS de.mpicbg.scicomp:joblist:0.6 de.mpicbg.scicomp:kutils:0.3
// add docopts to local m2 index
// git clone https://github.com/docopt/docopt.java && cd docopt.java && mvn clean package install -Dmaven.test.skip=true
// kotlinc-jvm -classpath $(mvncp org.docopt:docopt:0.6.0-SNAPSHOT)
import de.mpicbg.scicomp.kutils.evalBash
import joblist.JobConfiguration
import joblist.JobList
import kutils.evalBash
import org.docopt.Docopt
import java.io.File
......@@ -94,7 +94,7 @@ for (fastqFile in fastqFiles) {
// --quantMode GeneCounts see https://groups.google.com/forum/#!searchin/rna-star/GeneCounts/rna-star/gZRJx3ElRNo/p5FjBYKuY00J
// --outSJfilterCountUniqueMin see https://groups.google.com/forum/#!topic/rna-star/_1BeAlGUmpA
val isPE = with(fastqFile.name) { endsWith("_1.fastq.gz") || endsWith("_1.fastq") };
val isPE = with(fastqFile.name) { endsWith("_1.fastq.gz") || endsWith("_1.fastq") }
var fastqBaseName = fastqFile.name.removeSuffix(".gz").removeSuffix(".fastq")
if(isPE) fastqBaseName = fastqBaseName.removeSuffix("_1")
......
......@@ -27,7 +27,7 @@
<dependency>
<groupId>de.mpicbg.scicomp</groupId>
<artifactId>kutils</artifactId>
<version>0.2-SNAPSHOT</version>
<version>0.3</version>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlin</groupId>
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment