Workflow: Gathered Downsample and HaplotypeCaller

Fetched 2023-01-04 10:48:32 GMT
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Inputs

ID Type Title Doc
intervals e607da6f86b460defc850361159ea602[]

arrays of intervals to use in each individual run of the haplotypecaller

reference File

The reference that was used for the already-completed alignments

read_filter String (Optional)
downsample_seed Integer (Optional)
variant_index_type
crams_to_downsample https://w3id.org/cwl/view/git/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/pipelines/gathered_downsample_and_recall.cwl#crams_to_downsample/crams[]
downsample_strategy
max_alternate_alleles Integer (Optional)
qc_minimum_base_quality Integer
variant_index_parameter String (Optional)
emit_reference_confidence
qc_minimum_mapping_quality Integer

Steps

ID Runs Label Doc
join_results
gathered_downsample_and_recall.cwl#join_results/bfa9de02-d96e-40fc-8596-8be2d6ad1a78 (ExpressionTool)
gather_results
../tools/gather_to_sub_directory.cwl (CommandLineTool)
downsample_and_recall Downsample and HaplotypeCaller

Outputs

ID Type Label Doc
result_directories Directory[]
Permalink: https://w3id.org/cwl/view/git/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/pipelines/gathered_downsample_and_recall.cwl