- 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/7a2864f5af7723657406e4f3e94f92db09ec90fc/setup/cwl/module-4.cwl