- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
intervals | b65ce784af66008931634d7eafcf841e[] |
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/8eb189a4a34dc8cd86380685f814c79a444a7601/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/4e50d669-60f7-4259-a6e5-199220dec36c
(ExpressionTool)
|
||
gather_results |
../tools/gather_to_sub_directory.cwl
(CommandLineTool)
|
||
downsample_and_recall |
downsample_and_recall.cwl
(Workflow)
|
Downsample and HaplotypeCaller |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
result_directories | Directory[] |
Permalink:
https://w3id.org/cwl/view/git/8eb189a4a34dc8cd86380685f814c79a444a7601/definitions/pipelines/gathered_downsample_and_recall.cwl