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wodanaz / Assembling_viruses

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Use 4 cores for trim_galore #77

Closed johnbradley closed 2 years ago

johnbradley commented 2 years ago

Speed up remove_adapters/trim_galore by specifying 4 cores. Using 4 cores based on the suggestion in the trim_galore documentation.

Fixes #76

johnbradley commented 2 years ago

I was concerned that we might need to increase the number passed to the run-escape-variants.sh -j argument due to these changes. This is not the case. Increasing the number of threads for a step doesn't count towards the total number of jobs. The reason I was concerned is we were passing the value from jobs to the snakemake --cores parameter. The --cores parameter for snakemake is poorly named and should really be --jobs.

wodanaz commented 2 years ago

I was concerned that we might need to increase the number passed to the run-escape-variants.sh -j argument due to these changes. This is not the case. Increasing the number of threads for a step doesn't count towards the total number of jobs. The reason I was concerned is we were passing the value from jobs to the snakemake --cores parameter. The --cores parameter for snakemake is poorly named and should really be --jobs.

I see, and indeed some times is very confusing the nomenclature for jobs, threads, cores, cpus, etc. It seems some times they are used interchangeable sometimes not ;)