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How do I direct Queue to output files to a different directory?

louwslouws San FranciscoPosts: 12Member


Thanks to previous replies can run Queue and the relevant walker on a distributed computing server. The question was if I define my scala script to require an argument for the output file, using the -o parameter like so:

            // Required arguments.  All initialized to empty values.

             @Input(doc="Output file.", shortName="o")
                              var outputFile: File = _

How do I direct the output to pipe the result to a specified directory? Currently I have the code: genotyper.out = swapExt(qscript.bamFile, "bam", outputFile, "unfiltered.vcf")

Currently when I include the string -o /path/to/my/output/files/MyResearch.vcf

The script creates a series of folders within the directory where I execute Queue from. In this case my results were sent to: /Queue-2-8-1-g932cd3a/MyResearch./path/to/my/output/files/MyResearch.unfiltered.vcf

when all I wanted was the output to appear in the path: /path/to/my/output/files/MyResearch.unfiltered.vcf

As always any help is much appreciated.

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