# 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)