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tgen / pegasusPipe

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mergeVCFAlleleCount is not checking correctly if the job is already submitted #5

Closed tgenahmet closed 7 years ago

tgenahmet commented 7 years ago

merge VCF allele count is checking the wrong file to decide whether to submit the job. I think this causes the job to be submitted over and over again.

PedalheadPHX commented 7 years ago

@tgenahmet In the pegasus pipe there are two VCF merge steps. There is the version that does it on the somatic VCFs (Seurat, Strelka, MuTect) using code developed by Christophe and myself. Then there is a germline/constitutional merge of (Samtools, Haplotypecaller, and Freebayes) written by Megan. Just want to be sure we are not crossing these two independent events.

tgenahmet commented 7 years ago

Thanks for this info. I'll explore more and make sure this is not breaking anything.

denriquez commented 7 years ago

I see what you mean Ahmet. It is using this variable ${seurat_basename} as the name for the file it looks for and this variable is never initialized.

denriquez commented 7 years ago

So it should be replaced with $usableName