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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
The script creates a series of folders within the directory where I execute Queue from. In this case my results were sent to:
when all I wanted was the output to appear in the path:
As always any help is much appreciated.