Workflow: tmb.cwl
Fetched 2023-01-09 16:59:55 GMT
Verified with cwltool version 3.1.20221201130942
Workflow for calculating TMB tumor mutational burden on a single sample
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| normal_id | String | ||
| sample_id | String | ||
| assay_coverage | String |
genome_coverage value; amount of the genome in bp covered by the assay |
|
| mutations_file | File |
File with mutations for the sample |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| add_sampleID |
paste-col.cwl
(CommandLineTool)
|
||
| calc_tmb_value |
calc-tmb.cwl
(CommandLineTool)
|
||
| fix_tmb_header |
add_header.cwl
(CommandLineTool)
|
||
| filter_variants |
tmb_variant_filter.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad/cwl/tmb.cwl
