Workflow: igv-report_maf_workflow.cwl
Fetched 2025-04-30 15:10:30 GMT
Verified with cwltool version 3.1.20230201224320
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam_files | File[] | ||
| maf_files | File[] | ||
| ref_fasta | File | ||
| sites_maf | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| make_report |
igv-reports.cwl
(CommandLineTool)
|
||
| convert_mafs_to_vcf |
maf2vcf_gz_workflow.cwl
(Workflow)
|
Workflow to convert a maf file into a vcf.gz with .tbi index |
|
| convert_sites_to_vcf |
maf2vcf_gz_workflow.cwl
(Workflow)
|
Workflow to convert a maf file into a vcf.gz with .tbi index |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/59b69eed7ffefcffd81313ec8ffb84c0d716b933/cwl/igv-report_maf_workflow.cwl
