Workflow: tmb_workflow.cwl
Fetched 2024-10-25 09:03:11 GMT
Verified with cwltool version 3.1.20230201224320
Workflow to run the TMB analysis on a batch of samples and merge the results back into a single data clinical file
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| pairs | e0c93dc8c4eeb172d3d3e0e4b2f2dd32[] | ||
| assay_coverage | String |
genome_coverage value; amount of the genome in bp covered by the assay |
|
| data_clinical_file | File |
data clinical samplesheet file to merge the TMB results into |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_tmb_workflow |
tmb.cwl
(Workflow)
|
Workflow for calculating TMB tumor mutational burden on a single sample |
|
| concat_tmb_tables |
concat-tables_dir.cwl
(CommandLineTool)
|
Concatenate all the table files provided, but put the input files in a dir first to try avoiding issues with gigantic CLI args when tons of files are passed. |
|
| merge_data_clinical |
merge-tables.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/5cad957fec135aa55ca8d588372db0557ca1cad5/cwl/tmb_workflow.cwl
