blob: 2939db4d64ca360927bc30495d873394134bc91c (
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
|
# This is an example tumour-normal calling pipeline using strelka
{ bionix ? import <bionix> {}
, normal
, tumour
, ref
}:
with bionix;
with lib;
let
input = mapAttrs (_: fetchFastQGZ);
preprocess = pipe [
input
(bwa.align { ref = fetchFastA ref; })
(samtools.fixmate {})
(samtools.sort {})
(samtools.markdup {})
];
in linkDrv [
(ln (strelka.call {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka")
(ln (preprocess normal) "normal.bam")
(ln (preprocess tumour) "tumour.bam")
]
|
