
ThyagoLC
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MarkDuplicates using more cpus than allowed
Hello, I'm running the GATK RNAseq Best Practices workflow locally on our server. I'm only allowed to use 60 threads. However, during Picard MarkDuplicates, the tool uses all available CPU resource...
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Help with running GATK RNAseq workflow with docker backend and multiple cpus?
How do I configure the workflow to automatically run every tool with docker with more threads/cpus? I'm having a hard time. I'm using this docker.conf inside my backend section and set it as defaul...
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Avoid re-doing STAR references in RNAseq Germline variant workflow
AnsweredHow do I stop STAR from generating a new reference each time the workflow is run on a sample? Everytime I run gatk4-rnaseq-germline-snps-indels for each sample, the STAR reference step is created ...