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# 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)
]
|
