Set --threads to kraken2 (and check other tools).

MDU-PHL / bohra

A pipeline for bioinformatics analysis of bacterial genomes

GNU General Public License v3.0

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Set --threads to kraken2 (and check other tools). #44

Closed andersgs closed 3 years ago

andersgs commented 3 years ago

This will allow Kraken2 to play nicer with the Snkakemake scheduler.

abcdtree commented 3 years ago

Two main Risks in Bohra

kraken2 --paired {r1} {r2} --minimum-base-quality 13 --report {isolate}/kraken2.tab --memory-mapping --db {db} --threads NUM Number of threads (default: 18) Risk: using default threads Num 18

abriTAMR -c {input_file} -pfx {isolate} -w {w} --jobs JOBS, -j JOBS Number of AMR finder jobs to run in parallel. (default: 16) Risk: using default threads Num 16

These two may need to add Threads parameters from Snakemake rule.

@kristyhoran

Josh