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NBISweden / GenErode

GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
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Rewrite memory allocation for java-based tools (e.g. qualimap) #26

Open verku opened 2 years ago

verku commented 2 years ago

resources: mem_mb=lambda wildcards, input, threads, attempt: 6000 * threads - 2000

unset DISPLAY qualimap bamqc -bam {input.bam} --java-mem-size=${resources.mem_mb}M -nt {threads} -outdir {output}

or: def qualimap_mem(wildcards, input, threads, attempt): return 6000 * threads - 2000

resources: mem_mb=qualimap_mem