- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
sv_vcfs | File[] | ||
snps_vcf | File (Optional) | ||
same_type | Boolean | ||
cohort_name | String (Optional) | ||
same_strand | Boolean | ||
genome_build | String | ||
minimum_sv_size | Integer | ||
minimum_sv_calls | Integer | ||
estimate_sv_distance | Boolean | ||
max_distance_to_merge | Integer |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
bcftools_merge_sv_vcfs |
../tools/bcftools_merge.cwl
(CommandLineTool)
|
||
survivor_merge_sv_vcfs |
../tools/survivor.cwl
(CommandLineTool)
|
Run SURVIVOR to merge SV calls | |
bcftools_annotsv_filter |
../tools/annotsv_filter.cwl
(CommandLineTool)
|
filter AnnotSV tsv output generated from a bcftools merged vcf | |
bcftools_annotate_variants |
../tools/annotsv.cwl
(CommandLineTool)
|
||
survivor_annotate_variants |
../tools/annotsv.cwl
(CommandLineTool)
|
||
bcftools_bgzip_merged_sv_vcf |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
survivor_bgzip_merged_sv_vcf |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
bcftools_merged_sv_vcf | File | ||
survivor_merged_sv_vcf | File | ||
bcftools_merged_annotated_tsv | File | ||
survivor_merged_annotated_tsv | File | ||
bcftools_merged_filtered_annotated_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/definitions/subworkflows/merge_svs.cwl