Workflow: TOPMed Alignment

Fetched 2021-01-17 21:47:27 GMT

A CWL wrapper of the TopMed alignment workflow described here: https://github.com/statgen/docker-alignment

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Inputs

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

Steps

ID Runs Label Doc
samtools_sort
steps/samtools-sort.cwl (CommandLineTool)
SAMtools Sort
topmed_align
steps/align.cwl (CommandLineTool)
Align 1.0
topmed_post_align
steps/post-align.cwl (CommandLineTool)
Post-align
topmed_pre_align
steps/pre-align.cwl (CommandLineTool)
Pre-align 1.0

Outputs

ID Type Label Doc
output File (Optional) Output CRAM file
Permalink: https://w3id.org/cwl/view/git/923ae325fa3a6d3ee3871539c65afa06ac86ac54/aligner/sbg-alignment-cwl/topmed-alignment.cwl