Workflow: TOPMed Alignment
Fetched 2025-12-22 01:52:46 GMT
Verified with cwltool version 3.1.20221201130942
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/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
