pipelines_gathered_downsample_and_recall.cwl - genome/analysis-workflows GitHub Wiki
Documentation for gathered_downsample_and_recall.cwl
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Overview
Gathered Downsample and HaplotypeCaller
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
The reference that was used for the already-completed alignments |
['string', 'File'] |
|
| crams_to_downsample |
|
|
{'type': 'array', 'items': {'type': 'record', 'name': 'crams', 'fields': {'cram': {'type': 'File'}, 'downsample_ratio': {'type': 'float', 'doc': 'the downsample ratio to use when reprocessing this CRAM'}, 'contamination': {'type': 'float', 'doc': 'contamination score to pass to HaplotypeCaller'}}}} |
|
| downsample_strategy |
|
|
['null', {'type': 'enum', 'symbols': ['HighAccuracy', 'ConstantMemory', 'Chained']}] |
|
| downsample_seed |
|
|
int? |
|
| emit_reference_confidence |
|
|
{'type': 'enum', 'symbols': ['NONE', 'BP_RESOLUTION', 'GVCF']} |
|
| max_alternate_alleles |
|
|
int? |
|
| variant_index_type |
|
|
['null', {'type': 'enum', 'symbols': ['DYNAMIC_SEEK', 'DYNAMIC_SIZE', 'LINEAR', 'INTERVAL']}] |
|
| variant_index_parameter |
|
|
string? |
|
| read_filter |
|
|
string? |
|
| intervals |
|
arrays of intervals to use in each individual run of the haplotypecaller |
{'type': 'array', 'items': {'type': 'array', 'items': 'string'}} |
|
| qc_minimum_mapping_quality |
|
|
int |
|
| qc_minimum_base_quality |
|
|
int |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| result_directories |
|
|
Directory[] |
|
Steps