Workflow: workflow.cwl
Fetched 2023-01-04 23:26:56 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 |
|---|---|---|---|
| region | String | ||
| condition | String | ||
| windowsize | Integer | ||
| input_bam_file | File | ||
| input_vcf_file | File | ||
| output_filename | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter |
bcftools_filter.cwl
(CommandLineTool)
|
filter variants | |
| extract |
tabix_extract.cwl
(CommandLineTool)
|
extract region | |
| regions |
vcf_to_region.cwl
(CommandLineTool)
|
VCF to regions | |
| samtools_sort |
samtools_sort.cwl
(CommandLineTool)
|
sort bam | |
| samtools_view |
samtools_view.cwl
(CommandLineTool)
|
filter bam | |
| samtools_merge |
samtools_merge.cwl
(CommandLineTool)
|
merge bams |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| smallsortbam | File |
Permalink:
https://w3id.org/cwl/view/git/c2a178c4699cea6366284037dd96a66f377b7c58/bioinformatics/tools/workflow.cwl
