Workflow: tnscope-distr.cwl
Fetched 2024-04-16 23:37:34 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:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| pon | File (Optional) | ||
| qcal | File[] (Optional) | ||
| dbsnp | File (Optional) | ||
| given | File (Optional) | ||
| shard | String[] | ||
| cosmic | File (Optional) | ||
| phasing | Integer (Optional) | ||
| threads | Integer (Optional) | ||
| interval | File (Optional) | ||
| input_bam | File[] | ||
| reference | File | ||
| output_file | String | ||
| sv_mask_cmd | String (Optional) | ||
| sv_mask_ext | Integer (Optional) | ||
| prune_factor | Integer (Optional) | ||
| tumor_sample | String (Optional) | ||
| min_base_qual | Integer (Optional) | ||
| min_tumor_lod | Double (Optional) | ||
| normal_sample | String (Optional) | ||
| min_normal_lod | Double (Optional) | ||
| pcr_indel_model | String (Optional) | ||
| advanced_options | String[] (Optional) | ||
| min_init_tumor_lod | Double (Optional) | ||
| min_init_normal_lod | Double (Optional) | ||
| min_dbsnp_normal_lod | Double (Optional) | ||
| tumor_contamination_frac | Double (Optional) | ||
| normal_contamination_frac | Double (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tnscope |
../algo/tnscope.cwl
(CommandLineTool)
|
||
| sv_solver |
../algo/tnscope.cwl
(CommandLineTool)
|
||
| merge_pre_output |
../algo/tnscope.cwl
(CommandLineTool)
|
||
| merge_sv_data_tmp_output |
../algo/tnscope.cwl
(CommandLineTool)
|
||
| merge_sv_mate_tmp_output |
../algo/tnscope.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/stage/tnscope-distr.cwl
