Workflow: TOPMed Alignment

Fetched 2023-01-13 16:09:02 GMT

A CWL wrapper of the TopMed alignment workflow described here: https://github.com/statgen/docker-alignment Tool Author: Hyun Min Kang (hmkang@umich.edu) and Adrian Tan (atks@umich.edu) Wrapper Author: Marko Zecevic (marko.zecevic@sbgenomics.com)

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Inputs

ID Type Title Doc
dbsnp File (Optional) dbSNP VCF file
ram_min Integer (Optional) Minimum amount of RAM
threads Integer (Optional) Number of threads
bwa_index File BWA Index
cores_min Integer (Optional) Minimum number of cores
decomp_ref File (Optional) Reference for input CRAM decompressing
input_file File Input CRAM file
reference_genome File Reference for output CRAM compressing

Steps

There are no steps in this workflow

Outputs

ID Type Label Doc
output File (Optional) Output CRAM file
Permalink: https://w3id.org/cwl/view/git/d563c5137aa6d335625e4431f276563de61a5f90/aligner/sbg-alignment-cwl/topmed-alignment.cwl