blob: a5e497e680cce42d547ca5519374e0908f0d917a (
plain)
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
36
37
38
39
40
|
{ bionix
, indexAttrs ? {}
, bamIndexAttrs ? {}
, flags ? null
}:
inputs:
with bionix;
with lib;
with types;
let
filename = path: last (splitString "/" path);
getref = f: matchFiletype "platypus-callVariants" { bam = {ref, ...}: ref; } f;
refs = map getref inputs;
ref = head refs;
in
assert (length (unique refs) == 1);
stage {
name = "platypus";
buildInputs = with pkgs; [ platypus ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
ls -l
platypus callVariants \
--nCPU=$NIX_BUILD_CORES \
--refFile=ref.fa \
${optionalString (flags != null) flags} \
-o $out \
--bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
'';
passthru.filetype = filetype.vcf {ref = ref;};
}
|
