Workflow: calculate_contamination_workflow.cwl
Fetched 2026-01-15 19:16:00 GMT
Verified with cwltool version 3.1.20230201224320
GATK4.1.2 Calculate tumor-normal contamination 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 |
|---|---|---|---|
| intervals | File | ||
| java_heap | String | ||
| reference | File | ||
| tumor_bam | File | ||
| has_normal | Integer[] | ||
| normal_bam | File (Optional) | ||
| output_prefix | String | ||
| common_variant_reference | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| get_tumor_pileups |
../tools/calculate_contamination/get_pileup_summaries.cwl
(CommandLineTool)
|
||
| get_normal_pileups |
../tools/calculate_contamination/get_pileup_summaries.cwl
(CommandLineTool)
|
||
| extract_normal_pileups |
../utils-cwl/extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| calculate_contamination |
../tools/calculate_contamination/calculate_contamination.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| contamination_table | File | ||
| tumor_segments_table | File |
Permalink:
https://w3id.org/cwl/view/git/02129060b3a92f90daf1328f21b9db49da7a5aca/subworkflows/calculate_contamination_workflow.cwl
