started pe-aligner wrapper

dge_workflow/star_align.kts

+#!/usr/bin/env kscript
+//DEPS org.docopt:docopt:0.6.0-SNAPSHOT de.mpicbg.scicomp:joblist:0.6-SNAPSHOT de.mpicbg.scicomp.bioinfo:kutils:0.1-SNAPSHOT
+
+// 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 $(mvncp org.docopt:docopt:0.6.0-SNAPSHOT)
+
+// update joblist
+// cd ~/mnt/mack/bioinfo/holger/misc/Dropbox/cluster_sync/joblist/
+
+
+import joblist.JobConfiguration
+import joblist.JobList
+import kutils.bashEval
+import org.docopt.Docopt
+import java.io.File
+import java.util.*
+
+//val args = listOf("/projects/bioinfo/igenomes/Drosophila_melanogaster/Ensembl/BDGP6", "test.fastq.gz")
+
+
+// basic usage tutorial
+// http://www.homolog.us/blogs/blog/2012/11/02/star-really-kick-ass-rna-seq-aligner/
+
+
+// https://www.biostars.org/p/91020/
+
+val usage = """
+Use star to align fastq files against a genome
+Usage: star_align.sh [options] <igenome> <fastq_files>...
+
+Options:
+--gtf <gtfFile>     Custom gtf file instead of igenome bundled copy
+--pc-only           Use protein coding genes only for mapping and quantification
+"""
+
+
+val doArgs = Docopt(usage).parse(args.toList()).map {
+    it.key.removePrefix("--").replace("[<>]", "") to it.value?.toString()
+}.toMap()
+
+
+println(Objects.toString(1))
+println(Objects.nonNull(true))
+
+
+// extract all configuration parameters
+val fastqFiles = (doArgs["fastq_files"] as String).split(" ").map { File(it) }
+val igenome = File(doArgs["igenome"])
+val star_index = File(igenome, "Sequence/StarIndex")
+val gtfFile = if (doArgs["gtfFile"] != null) File(doArgs["gtfFile"]) else File(igenome, "Annotation/Genes/genes.gtf")
+
+// check if gtf file exists
+if (!gtfFile.isFile()) throw IllegalArgumentException("gtf '${gtfFile}' does not exist")
+
+// make sure that STAR is in the PATH
+if (bashEval("which STAR").exitCode != 0) throw IllegalArgumentException("gtf '${gtfFile}' does not exist")
+
+// Check if STAR index is not present
+if (!File("${star_index}/SA").isFile())
+    throw IllegalArgumentException("Missing STAR for ${star_index}/SA; use 'dge_create_star_index ${igenome}' to create it")
+//   dge_create_star_index ${igenome}'
+
+println("running STAR using igenome '${igenome}' for the following files")
+
+val jl = JobList(".starjobs")
+//rm .starjobs
+
+//fastqFiles=$(ls $baseDir/treps_pooled/*fastq.gz)
+
+for (fastqFile in fastqFiles) {
+    println("submitting STAR job for $fastqFile")
+
+    // uniquely mapping reads only:   http:/seqanswers.com/forums/showthread.php?s=93da11109ae12a773a128a637d69defe&t=3464
+    //#     tophat -p6  -G $gtfFile -g1 -o test $bowtie_gindex $fastqFile
+
+    // params:
+    // --outSAMstrandField intronMotif is required for cuffdiff compatiblity (xs flag)
+    // --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout to get rid of artifical junctions
+    // --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 fastqBaseName = fastqFile.name.replace(".fastq.gz", "")
+
+    val cmd = """
+    STAR --genomeDir $star_index --readFilesIn $fastqFile --runThreadN 6 --readFilesCommand zcat --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile $gtfFile --outFilterIntronMotifs   RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3
+    mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam
+    samtools index ${fastqBaseName}.bam
+    """.trimIndent()
+
+    jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", null, "medium", 5, "", better.files.File(File(".").toPath())))
+}
+
+
+jl.waitUntilDone(1000)
+//val requiresRerun: List<Job>? = jl.requiresRerun().
+//if (requiresRerun.istEmpty()) throw RuntimeException("jobs failed: \n" +jl.printStatus())
+
+
+// http://lampwww.epfl.ch/~michelou/scala/using-scala-from-java.html
+joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport()
+
+
+//// estimate expresssion with http://bioinf.wehi.edu.au/featureCounts/
+////Summarize multiple datasets at the same time:
+//#featureCounts - t exon -g gene_id -a annotation.gtf -o counts.txt library1.bam library2.bam library3.bam
+//
+//// FeatureCounts --> Commented out because now part of STAR
+//#bamFile = control_3.bam
+//#featureCounts - t exon -g gene_id -a ${ gtfFile } - o feature_counts.txt ${ bamFile } - T 5
+//#mysub "${project}__feature_counts" "featureCounts -t exon -g gene_id -a ${gtfFile} -o gene_counts.txt $(ls *bam) -T 5"-q medium | blockScript
+//
+
+
+// cleanup
+bashEval("""rm - rf * STARgenome * .Log.progress.out _STARtmp * .SJ.out.tab *Log.out""")
+
+// Test for bam correlation (but don't wait for the results)
+bashEval("""
+rend.R - e ${ System.getenv("NGS_TOOLS") } / dge_workflow / star_qc.R.
+dge_bam_correlate &
+""")
+
+// Condense counts into matrix
+bashEval("""dge_star_counts2matrix""")

pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>ngs_tools</artifactId>
+    <groupId>de.mpicbg.scicomp.bioinfo</groupId>
+    <version>1.0-SNAPSHOT</version>
+
+
+    <dependencies>
+        <dependency>
+            <groupId>org.docopt</groupId>
+            <artifactId>docopt</artifactId>
+            <version>0.6.0-SNAPSHOT</version>
+        </dependency>
+
+        <dependency>
+            <groupId>de.mpicbg.scicomp</groupId>
+            <artifactId>joblist_2.11</artifactId>
+            <version>0.6-SNAPSHOT</version>
+        </dependency>
+
+        <dependency>
+            <groupId>de.mpicbg.scicomp.bioinfo</groupId>
+            <artifactId>kutils</artifactId>
+            <version>0.1-SNAPSHOT</version>
+        </dependency>
+    </dependencies>
+</project>
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