Commit d35a71dd authored by Holger Brandl's avatar Holger Brandl

updated dependencies

parent 72893bc8
#!/usr/bin/env kscript #!/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 // 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 // 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) // kotlinc-jvm -classpath $(mvncp org.docopt:docopt:0.6.0-SNAPSHOT)
import de.mpicbg.scicomp.kutils.evalBash
import joblist.JobConfiguration import joblist.JobConfiguration
import joblist.JobList import joblist.JobList
import kutils.evalBash
import org.docopt.Docopt import org.docopt.Docopt
import java.io.File import java.io.File
...@@ -94,7 +94,7 @@ for (fastqFile in fastqFiles) { ...@@ -94,7 +94,7 @@ for (fastqFile in fastqFiles) {
// --quantMode GeneCounts see https://groups.google.com/forum/#!searchin/rna-star/GeneCounts/rna-star/gZRJx3ElRNo/p5FjBYKuY00J // --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 // --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") var fastqBaseName = fastqFile.name.removeSuffix(".gz").removeSuffix(".fastq")
if(isPE) fastqBaseName = fastqBaseName.removeSuffix("_1") if(isPE) fastqBaseName = fastqBaseName.removeSuffix("_1")
......
...@@ -27,7 +27,7 @@ ...@@ -27,7 +27,7 @@
<dependency> <dependency>
<groupId>de.mpicbg.scicomp</groupId> <groupId>de.mpicbg.scicomp</groupId>
<artifactId>kutils</artifactId> <artifactId>kutils</artifactId>
<version>0.2-SNAPSHOT</version> <version>0.3</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.jetbrains.kotlin</groupId> <groupId>org.jetbrains.kotlin</groupId>
......
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