Workflow: Gathered Downsample and HaplotypeCaller

Fetched 2023-01-10 03:36:55 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs variant_index_parameter variant_index_parameter downsample_and_recall Downsample and HaplotypeCaller variant_index_parameter->downsample_and_recall variant_index_parameter crams_to_downsample crams_to_downsample gather_results gather_results crams_to_downsample->gather_results outdir crams_to_downsample->downsample_and_recall crams_to_downsample intervals intervals intervals->downsample_and_recall intervals variant_index_type variant_index_type variant_index_type->downsample_and_recall variant_index_type emit_reference_confidence emit_reference_confidence emit_reference_confidence->downsample_and_recall emit_reference_confidence downsample_strategy downsample_strategy downsample_strategy->downsample_and_recall downsample_strategy 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 downsample_seed downsample_seed downsample_seed->downsample_and_recall downsample_seed read_filter read_filter read_filter->downsample_and_recall read_filter qc_minimum_mapping_quality qc_minimum_mapping_quality qc_minimum_mapping_quality->downsample_and_recall qc_minimum_mapping_quality reference reference reference->downsample_and_recall reference result_directories result_directories join_results join_results join_results->gather_results files gather_results->result_directories downsample_and_recall->join_results wgs_metrics downsample_and_recall->join_results gvcfs
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Inputs

ID Type Title Doc
intervals fb766a6281cdeaf37745daaf4ccccf9a[]

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/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/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/1df6acb1-2795-4e04-83d9-2029229a2377 (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/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/gathered_downsample_and_recall.cwl