- 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/8d9c9155a49045762cbf5a1e584fc20517b8be87/cwl/workflows/gatk-4.0.0.0-haplotypecaller.cwl