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Generalizing the FullProcessingPipeline Qscript 

We have generalized the processing script to be able to handle multiple scenarios. Originally it was
designed for PCR free data only, we added all the steps necessary to start from fastq and process
RNA-seq as well as non-human data. This is our go to script in TechDev.

   * add optional "starting from fastq" path to the pipeline
   * add mark duplicates (optionally) to the pipeline
   * add an option to run with the mouse data (without dbsnp and with single ended fastq)
   * add option to process RNA-seq data from topHat (add RG and reassign mapping quality if necessary)
   * add option to filter or include reads with N in the cigar string
   * add parameter to allow keeping the intermediate files
This commit is contained in:
Mauricio Carneiro 2013-08-22 22:18:47 -04:00
parent f15355856a
commit 725656ae7e
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
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@ -325,7 +325,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
* @throws IOException If the file cannot be written.
*/
private void writeFile(String fullClassName, String content) throws IOException {
File outputFile = new File(outputDirectory, fullClassName.replace(".", "/") + ".scala");
File outputFile = new File(outputDirectory, fullClassName.replace(".", "/") + "MoleculoPipeline.scala");
if (outputFile.exists()) {
String existingContent = FileUtils.readFileToString(outputFile);
if (StringUtils.equals(content, existingContent))