blob: 4f00431f5e84333a0ea5d481beac9be5c5101724 (
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
|
# This is a translation of the Nextflow example found at
# https://www.nextflow.io/example1.html
{ bionix ? import ./../.. {}
, input ? ./sample.fa}:
with bionix;
with lib;
let
splitSequences = fa: stage {
name = "splitSequences";
buildInputs = [ pkgs.gawk ];
buildCommand = ''
awk '/^>/{f="seq_"++d} {print > f}' ${fa}
mkdir $out
cp seq* $out
'';
};
reverse = fa: stage {
name = "reverse";
buildCommand = ''
${pkgs.utillinux}/bin/rev ${fa} > $out
'';
};
in pipe input [
splitSequences
(each reverse)
]
|
