Workflow: Gathered Downsample and HaplotypeCaller
Fetched 2025-07-15 06:36:56 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
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- 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 | 360804ca135209beebdffb7af362b8a8[] |
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/5fda2d9eb52a363bd51011b3851c2afb86318c0c/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/f4a9dc13-c2f3-4788-b241-9bf7deb8d5e2
(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/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/pipelines/gathered_downsample_and_recall.cwl
