Workflow: gatk-4.0.0.0-haplotypecaller.cwl
Fetched 2024-04-24 10:23:35 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| chunks | Integer | ||
| ploidy | Integer | ||
| pcr_free | Boolean | ||
| library_cram | File | ||
| intersect_file | File | ||
| reference_dict | File | ||
| reference_fasta | File | ||
| include_chromosome_regex | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| intersect |
intersect_intervals.cwl
(Workflow)
|
||
| split_interval_list |
../tools/split_interval_list.cwl
(CommandLineTool)
|
||
| filter_interval_list |
../tools/filter_interval_list.cwl
(CommandLineTool)
|
||
| dict_to_interval_list |
../tools/dict_to_interval_list.cwl
(CommandLineTool)
|
||
| combine_haplotype_index |
../expression-tools/combine_files.cwl
(ExpressionTool)
|
Step to put secondary input files in the same folder as a main file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| intervals | File[] | ||
| gvcf_files | File[] |
Permalink:
https://w3id.org/cwl/view/git/c822e40575ecd7fc65626a73363f3bbc193b9a74/cwl/workflows/gatk-4.0.0.0-haplotypecaller.cwl
