ThyagoLC
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Activity overview
Latest activity by ThyagoLC-
ThyagoLC commented,
Just to let others know that writing a script to run cpulimit on java worked. It controlled the cpu usage of all GATK tools invoked downstream by the workflow without problems. Thanks
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ThyagoLC created a post,
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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ThyagoLC commented,
Genevieve Brandt (she/her), Thanks! Got it. So the problem is that other than STAR, those other Picard tools don't support multi-threading, so I can't pass multiple cpus in runtime section unlike l...
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ThyagoLC created a post,
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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ThyagoLC commented,
Hi Samantha (she/her) I found out about the zippedStarReferences input later on, thank you! As for the second question, I'll leave my solution below so others may benefit from it: I used a custom ....
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ThyagoLC created a post,
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 ...