# 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 <bionix> {}
,inputs
,ref ? bionix.ref.grch38.seq }:

with bionix;
with lib;

let
  preprocess = flip pipe [
    (bwa.align { inherit ref; })
    (samtools.fixmate {})
    (samtools.sort {})
    (samtools.markdup {})
  ];

in platypus.call {} (map preprocess inputs)