blob: ad659de8d4b7b4cb8c69f00e89548678c2dde89e (
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
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
|
{ bionix
, blacklist ? null
, bwaIndexAttrs ? { }
, faidxAttrs ? { }
, flags ? null
, config ? null
, heapSize ? "31g"
}:
with bionix;
with lib;
with types;
inputs:
let
getref = matchFiletype "gridss-callVariants" { bam = x: x.ref; };
refs = map getref inputs;
ref = head refs;
in
assert (length (unique refs) == 1);
stage rec {
name = "gridss-callVariants";
buildInputs = with pkgs; [ jre R bwa ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
ln -s $f
done
mkdir $out
java -ea -Xmx${heapSize} \
-Dreference_fasta="ref.fa" \
-Dsamjdk.create_index=true \
-Dsamjdk.use_async_io_read_samtools=true \
-Dsamjdk.use_async_io_write_samtools=true \
-Dsamjdk.use_async_io_write_tribble=true \
-Dgridss.gridss.output_to_temp_file=true \
-cp ${bionix.gridss.jar} gridss.CallVariants \
VERBOSITY=WARNING \
WORKER_THREADS=$NIX_BUILD_CORES \
TMP_DIR=. \
WORKING_DIR=. \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
REFERENCE_SEQUENCE="ref.fa" \
${concatMapStringsSep " " (i: "INPUT=\"${i}\"") inputs} \
OUTPUT="$out/gridss.vcf" \
ASSEMBLY="$out/gridss.bam" \
${optionalString (blacklist != null) ("BLACKLIST=" + blacklist)} \
${optionalString (flags != null) flags}
# The VCF index is non-deterministic
rm $out/gridss.vcf.idx
'';
passthru.multicore = true;
}
|
