Workflow: Gathered Downsample and HaplotypeCaller

Fetched 2023-01-10 01:25:10 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs qc_minimum_mapping_quality qc_minimum_mapping_quality downsample_and_recall Downsample and HaplotypeCaller qc_minimum_mapping_quality->downsample_and_recall qc_minimum_mapping_quality downsample_seed downsample_seed downsample_seed->downsample_and_recall downsample_seed downsample_strategy downsample_strategy downsample_strategy->downsample_and_recall downsample_strategy crams_to_downsample crams_to_downsample crams_to_downsample->downsample_and_recall crams_to_downsample gather_results gather_results crams_to_downsample->gather_results outdir emit_reference_confidence emit_reference_confidence emit_reference_confidence->downsample_and_recall emit_reference_confidence intervals intervals intervals->downsample_and_recall intervals read_filter read_filter read_filter->downsample_and_recall read_filter variant_index_type variant_index_type variant_index_type->downsample_and_recall variant_index_type reference reference reference->downsample_and_recall reference variant_index_parameter variant_index_parameter variant_index_parameter->downsample_and_recall variant_index_parameter qc_minimum_base_quality qc_minimum_base_quality qc_minimum_base_quality->downsample_and_recall qc_minimum_base_quality max_alternate_alleles max_alternate_alleles max_alternate_alleles->downsample_and_recall max_alternate_alleles result_directories result_directories join_results join_results join_results->gather_results files downsample_and_recall->join_results gvcfs downsample_and_recall->join_results wgs_metrics gather_results->result_directories
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Inputs

ID Type Title Doc
intervals c7bb4918031b9b6ae4f50b1dca5552de[]

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/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/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/7adfbea1-706b-4656-8bb5-8d46c32d020d (ExpressionTool)
gather_results
../tools/gather_to_sub_directory.cwl (CommandLineTool)
downsample_and_recall Downsample and HaplotypeCaller

Outputs

ID Type Label Doc
result_directories Directory[]
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/pipelines/gathered_downsample_and_recall.cwl