- 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 |
---|---|---|---|
ploidy | Integer (Optional) | ||
intervals | 540006dee3ccaa987582da17722529de[] |
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) | ||
crams_to_downsample | https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/pipelines/downsample_and_recall.cwl#crams_to_downsample/crams[] | ||
downsample_strategy | |||
max_alternate_alleles | Integer (Optional) | ||
qc_minimum_base_quality | Integer | ||
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 | 15ee558a44b9a32003a3b8e10d1ea37a[] | ||
wgs_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/pipelines/downsample_and_recall.cwl