Workflow: fusion_simulation_workflow.cwl
Fetched 2024-11-25 11:31:22 GMT
Verified with cwltool version 3.1.20221201130942
Fusion Simulation Workflow
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| GTF | File | ||
| SEED | Integer (Optional) | ||
| GENOME | File | ||
| SIM_NAME | String | ||
| DIP_GENOME | File | ||
| NUM_EVENTS | Integer | ||
| RSEM_MODEL | File | ||
| TARGET_DEPTH | Integer | ||
| MID_EXON_PROB | Float (Optional) | ||
| MID_EXON_MIN_SIZE | Integer (Optional) | ||
| EXPRESSION_PROFILE | File | ||
| MID_EXON_MIN_CLEAVED | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tar |
../general_tools/tar_extract.cwl
(CommandLineTool)
|
command line: tar |
|
| reads |
../fastq_create/cwl/create_fastq.cwl
(CommandLineTool)
|
Generate FastQ reads files |
|
| fusion |
../fusion_create/cwl/create_fusion.cwl
(CommandLineTool)
|
Create fusion events |
|
| gunzip |
../general_tools/gunzip.cwl
(CommandLineTool)
|
command line: gunzip. Note: gunzip is not a well behaved program by CWL standards. It creates a file in the input directory (not the output directory) and deletes the original file. Both of these are generally not allowed by CWL. This is a version of gunzip wrapper that works. |
|
| isoform |
../model_isoforms/cwl/model_isoforms.cwl
(CommandLineTool)
|
Model Isoform Expression |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| OUTPUT | File[] |
Permalink:
https://w3id.org/cwl/view/git/f621d09c48a6abfd2c63105a2c096f39a1627a07/workflow/fusion_simulation_workflow.cwl
