Workflow: pindel parallel workflow
Fetched 2024-11-23 23:09:52 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 |
|---|---|---|---|
| reference | File | ||
| tumor_bam | File | ||
| normal_bam | File | ||
| insert_size | Integer | ||
| min_var_freq | Float (Optional) | ||
| interval_list | File | ||
| scatter_count | Integer | ||
| tumor_sample_name | String | ||
| normal_sample_name | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| filter |
fp_filter.cwl
(Workflow)
|
fp_filter workflow | |
| cat_all |
../tools/cat_all.cwl
(CommandLineTool)
|
||
| reindex |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| pindel_cat |
pindel_cat.cwl
(Workflow)
|
Per-region pindel | |
| somaticfilter |
../tools/pindel_somatic_filter.cwl
(CommandLineTool)
|
pindel somatic filter | |
| remove_end_tags |
../tools/remove_end_tags.cwl
(CommandLineTool)
|
remove END INFO tags | |
| split_interval_list_to_bed |
../tools/split_interval_list_to_bed.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File | ||
| unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/656d9ae18f164f983c5672bcf51037cd73309f4f/subworkflows/pindel.cwl
