Workflow: TOPMed Alignment
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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- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 3-clause "New" or "Revised" License
Note that the tools invoked by the workflow may have separate licenses.
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