Workflow: Downsample and HaplotypeCaller
Fetched 2023-01-04 10:33:11 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
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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 |
|---|---|---|---|
| ploidy | Integer (Optional) | ||
| intervals | f3b13be41b9874b961a1327e60bb429a[] |
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/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/pipelines/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 |
|---|---|---|---|
| downsample |
../tools/downsample.cwl
(CommandLineTool)
|
downsample unaligned BAM | |
| haplotype_caller | scatter GATK HaplotypeCaller over intervals | ||
| collect_wgs_metrics |
../tools/collect_wgs_metrics.cwl
(CommandLineTool)
|
collect WGS metrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcfs | b743f06fc8322f0a3755f56bfd62ed38[] | ||
| wgs_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/pipelines/downsample_and_recall.cwl
