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nf-core / oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline
https://nf-co.re/oncoanalyser
MIT License
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Add option for Sambamba tmp directory #112

Open adbeggs opened 4 days ago

adbeggs commented 4 days ago

Description of feature

Hi

I've had multiple crashes on a Slurm based HPC environment as sambamba sort fills up the compute nodes /tmp directory and crashes out. Can you add a command line option to allow pre-specification of this? I have modified my bwamem2/main.nf for now which works

A