Workflow: hi-c-processing-pairs.cwl
Fetched 2024-11-23 22:57:19 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| nres | Integer | ||
| maxmem | String | ||
| nofrag | Boolean | ||
| higlass | Boolean | ||
| min_res | Integer | ||
| nthreads | Integer | ||
| chunksize | Integer | ||
| chromsizes | File | ||
| custom_res | String | ||
| juicer_res | Boolean | ||
| input_pairs | File[] (Optional) | ||
| max_split_cooler | Integer | ||
| restriction_file | File (Optional) | ||
| mapqfilter_juicer | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| cooler |
cooler.cwl
(CommandLineTool)
|
||
| pairs2hic |
pairs2hic.cwl
(CommandLineTool)
|
||
| cool2mcool |
cool2mcool.cwl
(CommandLineTool)
|
||
| merge-pairs |
merge-pairs.cwl
(CommandLineTool)
|
||
| addfragtopairs |
addfragtopairs.cwl
(CommandLineTool)
|
||
| add-hic-normvector-to-mcool |
add-hic-normvector-to-mcool.cwl
(CommandLineTool)
|
||
| extract-mcool-normvector-for-juicebox |
extract-mcool-normvector-for-juicebox.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| hic | File | ||
| mcool | File | ||
| merged_pairs | File | ||
| cooler_normvector | File |
Permalink:
https://w3id.org/cwl/view/git/895a101d06c26f8c7f8a63545b2b74921b5f7526/cwl_awsem_v1/hi-c-processing-pairs.cwl
