Commit 29bf997a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed filenames of bam files at star

parent 65a485aa
...@@ -90,7 +90,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri ...@@ -90,7 +90,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
} else if (aligner == "star") { } else if (aligner == "star") {
val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = qscript.outputDir + "star/"; init} val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = qscript.outputDir + "star/"; init}
add(starCommand) add(starCommand)
bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), swapExt(outputDir,starCommand.outputSam,".sam",".bam"), outputDir) bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), new File(outputDir + outputName + ".bam"), outputDir)
} else if (aligner == "star-2pass") { } else if (aligner == "star-2pass") {
val starCommand_pass1 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; val starCommand_pass1 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2;
this.outputDir = qscript.outputDir + "star-2pass/aln-pass1/"; init} this.outputDir = qscript.outputDir + "star-2pass/aln-pass1/"; init}
...@@ -103,7 +103,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri ...@@ -103,7 +103,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
val starCommand_pass2 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.deps ++= starCommand_reindex.outputs; val starCommand_pass2 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.deps ++= starCommand_reindex.outputs;
this.outputDir = qscript.outputDir + "star-2pass/aln-pass2/"; this.genomeDir = starCommand_reindex.outputDir; init} this.outputDir = qscript.outputDir + "star-2pass/aln-pass2/"; this.genomeDir = starCommand_reindex.outputDir; init}
add(starCommand_pass2) add(starCommand_pass2)
bamFile = addAddOrReplaceReadGroups(List(starCommand_pass2.outputSam), swapExt(outputDir,starCommand_pass2.outputSam,".sam",".bam"), outputDir) bamFile = addAddOrReplaceReadGroups(List(starCommand_pass2.outputSam), new File(outputDir + outputName + ".bam"), outputDir)
} else throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid") } else throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid")
if (!skipMarkduplicates) bamFile = addMarkDuplicates(List(bamFile), swapExt(outputDir,bamFile,".bam",".dedup.bam"), outputDir) if (!skipMarkduplicates) bamFile = addMarkDuplicates(List(bamFile), swapExt(outputDir,bamFile,".bam",".dedup.bam"), outputDir)
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