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{ bionix }:
with bionix;
with types;
{
/* Calls somatic variants
Type: callSomatic :: {...} -> {tumour, normal} -> somatic results
*/
callSomatic = callBionixE ./strelka-callSomatic.nix;
/* Calls variants
Type: call :: {...} -> [input] -> results
*/
call = callBionixE ./strelka-call.nix;
/* Extract VCF file from results
Type: variants :: results -> vcf
*/
variants =
# result of call
drv: stage {
name = "strelka-call-variants";
buildCommand = ''
ln -s ${drv}/variants/variants.vcf.gz $out
'';
passthru.filetype = filetype.gz (filetype.vcf {ref=ref;});
};
/* Extract indels from somatic results
Type: indels :: somatic results -> vcf
*/
indels =
# result of callSomatic
drv: stage {
name = "strelka-callVariants-indels";
buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf.gz $out";
passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});
};
/* Extract SNVs from somatic results
Type: snvs :: somatic results -> vcf
*/
snvs =
# result of callSomatic
drv: stage {
name = "strelka-callVariants-snvs";
buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf.gz $out";
passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});
};
}
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