Workflow: module-3
Fetched 2023-01-12 02:18:05 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bed | File | ||
| dbsnp | File | ||
| cosmic | File | ||
| genome | String | ||
| refseq | File | ||
| mutect_rf | String[] | ||
| ref_fasta | String | ||
| tumor_bam | File | ||
| normal_bam | File | ||
| facets_cval | Integer | ||
| hotspot_vcf | File | ||
| mutect_dcov | Integer | ||
| facets_pcval | Integer | ||
| tumor_sample_name | String | ||
| normal_sample_name | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index |
cmo-index/1.0.0/cmo-index.cwl
(CommandLineTool)
|
cmo-index | |
| concat |
bcftools.concat/1.3.1/bcftools.concat.cwl
(CommandLineTool)
|
concatenate VCF/BCF files from the same set of samples |
|
| filtering | |||
| call_variants | |||
| create_vcf_file_array |
module-3.cwl#create_vcf_file_array/aed8509c-a8c8-4819-9dbb-37d70f424792
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| facets_out | File[] | ||
| facets_png | File[] | ||
| facets_seg | File[] | ||
| mutect_vcf | File | ||
| pindel_vcf | File | ||
| combine_vcf | File | ||
| vardict_vcf | File | ||
| facets_rdata | File[] | ||
| facets_counts | File | ||
| mutect_norm_vcf | File | ||
| pindel_norm_vcf | File | ||
| mutect_callstats | File | ||
| vardict_norm_vcf | File | ||
| facets_txt_hisens | File | ||
| facets_txt_purity | File |
Permalink:
https://w3id.org/cwl/view/git/3ec29bfdcbc444c6599e484640cf83a7c5d91aaa/setup/cwl/module-3.cwl
