Workflow: fillout_workflow.cwl
Fetched 2024-10-30 08:41:26 GMT
Verified with cwltool version 3.1.20230201224320
Workflow to run GetBaseCountsMultiSample fillout on a number of bam files with a single maf file
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| maf_file | File |
The reference maf file with coordinates to run fillout against for each bam file |
|
| bam_files | File[] | ||
| ref_fasta | File | ||
| sample_ids | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fillout |
getbasecountsmultisample.cwl
(CommandLineTool)
|
Get the base counts in a .bam file for all the position in the supplied maf file |
|
| concat_mafs |
concat-mafs_all_cols.cwl
(CommandLineTool)
|
Version of concat-mafs.cwl that doesnt drop any columns or make columns blank |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/5cad957fec135aa55ca8d588372db0557ca1cad5/cwl/fillout_workflow.cwl
