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# This is an example pipeline specification to do multi-sample variant calling
# with the Platypus variant caller. Each input is preprocessed by aligning
# against a reference genome (defaults to GRCH38), fixing mate information, and
# marking duplicates. Finally platypus is called over all samples.
{bionix ? import ./.. {}
,inputs
,ref ? null}:
with bionix;
let
preprocess = pipe [
(bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;})
(samtools.fixmate {})
(samtools.sort {})
(samtools.markdup {})
];
in platypus.call {} (map preprocess inputs)
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