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{ bionix ? import <bionix> { }, tmpDir ? null }:
let
bionix' = (bionix."${if tmpDir == null then "slurm" else "qsub"}" {
ppn = 24;
mem = 7;
walltime = "3:00:00";
} // bionix.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; }).extend
(self: super:
with self; {
minimap2.align = def super.minimap2.align {
mem = 15;
walltime = "16:00:00";
};
samtools = super.samtools // (with super.samtools; {
markdup = def markdup { walltime = "12:00:00"; };
fixmate = def fixmate { walltime = "10:00:00"; };
sort = def sort {
mem = 27;
flags = "-m 1G";
};
});
});
in import ./. { bionix = bionix'; }
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