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…oadInstitute. The process runs verifyBamID to retrieve estimation table and calculate contamination float.
ellendejong
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Feb 23, 2021
rernst
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Feb 23, 2021
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Could you add this parameter and let nextflow set the number of threads based on the process cpus config.
--NumThread [Int] Set number of threads in likelihood calculation[default:4]
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@rernst Ratio threads:cpu is not 1:1 on the HPC, i believe. Do we use a scaling factor somewhere? |
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No we don't correct / adjust for hyperthreading, we just use |
rernst
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Apr 30, 2021
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What has changed?
A process is implemented to estimate DNA contamination.
Additional information
Azure backlog item: https://dev.azure.com/umcu/LAB-Bioinformatics-Genetics/_workitems/edit/63171
https://dev.azure.com/umcu/LAB-Bioinformatics-Genetics/_workitems/edit/66906
DxNextflowWes UMCUGenetics/DxNextflowWES#28
I keep track of to-do's in Azure and pull-request DxNextflowWes.