This pull request addresses #12, where the nf-core SPAdes module isn't sufficient for metagenomic assembly because of the memory label and doesn't run with metaspades option.
This replaces the nf-core SPAdes module with a local metaspades module where the metaspades.py script is called in SPAdes instead. This adds configuration to dynamically adjust memory and cpus based on the number of retries if a process exits because of out of memory status from SPAdes. This way the process label process_high_memory doesn't have to be applied to this process overall and can be adjusted on a sample-by-sample basis when going through this assembly process.
This pull request addresses #12, where the nf-core SPAdes module isn't sufficient for metagenomic assembly because of the memory label and doesn't run with
metaspadesoption.This replaces the
nf-coreSPAdes module with a localmetaspadesmodule where themetaspades.pyscript is called in SPAdes instead. This adds configuration to dynamically adjust memory and cpus based on the number of retries if a process exits because of out of memory status from SPAdes. This way the process labelprocess_high_memorydoesn't have to be applied to this process overall and can be adjusted on a sample-by-sample basis when going through this assembly process.