Workflow: module-4
Fetched 2026-09-09 16:05:29 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] | ||
| genome | String | ||
| db_files | |||
| vep_data | String | ||
| ref_fasta | String | ||
| runparams | |||
| exac_filter | File | ||
| annotate_vcf | File | ||
| curated_bams | String[] | ||
| hotspot_list | File | ||
| tumor_sample_name | String | ||
| normal_sample_name | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| vcf2maf |
cmo-vcf2maf/1.6.17/cmo-vcf2maf.cwl
(CommandLineTool)
|
cmo-vcf2maf |
None |
| ngs_filters |
ngs-filters/1.4/ngs-filters.cwl
(CommandLineTool)
|
ngs-filters |
This tool flags false-positive somatic calls in a given MAF file |
| remove_variants |
remove-variants/0.1.1/remove-variants.cwl
(CommandLineTool)
|
remove-variants |
Remove snps/indels from the output maf where a complex variant is called |
| fillout_normal_panel | |||
| fillout_tumor_normal |
cmo-fillout/1.2.2/cmo-fillout.cwl
(CommandLineTool)
|
cmo-fillout |
Fillout allele counts for a MAF file using GetBaseCountsMultiSample on BAMs |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| maf | File |
Permalink:
https://w3id.org/cwl/view/git/bffe2339db0b056a61514d75773f793920b6750e/setup/cwl/module-4.cwl
