tools/xenomapper-allocate.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
31
32
33
34
35

{ bionix
, flags ? null
}:

{ primary, secondary }:

with bionix;
with lib;
with types;

let

  isSortedBam = matchFiletype "xenomapper-allocate" { bam = matchSorting "xenomapper-allocate" { coord = _: false; name = _: true; none = _: false; }; };
  outs = [ "primary_specific" "primary_multi" "secondary_specific" "secondary_multi" "unassigned" "unresolved" ];

in

assert isSortedBam primary;
assert isSortedBam secondary;

stage {
  name = "xenomapper-allocate";
  buildInputs = with pkgs; [ samtools python3Packages.xenomapper ];
  outputs = [ "out" ] ++ outs;
  buildCommand = ''
    xenomapper ${optionalString (flags != null) flags} \
      --primary_bam ${primary} --secondary_bam ${secondary} \
      ${concatMapStringsSep " " (out: "--${out} >(samtools view -bS - > ${"$" + out})") outs}

    mkdir -p $out
    for x in ${concatStringsSep " " outs} ; do
      ln -s ''${!x} $out/$x.bam
    done
  '';
}