Workflow: downsample unaligned BAM and align

Fetched 2023-01-04 19:55:26 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
bams File[]
reference String
readgroups String[]
bqsr_known_sites File[]

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

downsample_probability Float

Steps

ID Runs Label Doc
downsample
../tools/downsample.cwl (CommandLineTool)
downsample unaligned BAM
align_workflow
bam_to_bqsr.cwl (Workflow)
Unaligned BAM to BQSR

Outputs

ID Type Label Doc
bam File
mark_duplicates_metrics_file File
Permalink: https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/subworkflows/downsampled_alignment.cwl