examples/ex-tnpair/cluster.nix


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

{ tmpDir ? null }:

let
  bionix = import <bionix> {
    overlays = [
      (_: super:
        super."${if tmpDir == null then "slurm" else "qsub"}" {
          ppn = 24;
          mem = 7;
          walltime = "3:00:00";
        } // super.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; })

      (self: super:
        with super; {
          minimap2.align = def minimap2.align {
            mem = 15;
            walltime = "16:00:00";
          };
          samtools = with 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 ./. { inherit bionix; }