Workflow: msi_workflow.cwl
Fetched 2023-01-09 11:55:57 GMT
Verified with cwltool version 3.1.20221201130942
Workflow to run the MSI 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 | d28bb90162110465e86b7f8a15bb1d6e[] | ||
| tumor_bam_files | File[] | ||
| normal_bam_files | File[] | ||
| data_clinical_file | File |
data clinical samplesheet file to merge the MSI results into |
|
| microsatellites_file | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| cut_msi_table |
cut.cwl
(CommandLineTool)
|
||
| replace_col_name |
replace_colname.cwl
(CommandLineTool)
|
||
| concat_msi_tables |
concat-tables.cwl
(CommandLineTool)
|
||
| add_msi_status_col |
add_msi_status.cwl
(CommandLineTool)
|
||
| merge_data_clinical |
merge-tables.cwl
(CommandLineTool)
|
||
| run_msi_add_sample_id |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/3bc4fab5503e58521ed0eb9c0d035ac18460dc13/cwl/msi_workflow.cwl
