Workflow: Perform SV calling of sample vs matched control using Delly, Lumpy, and Manta
Fetched 2024-11-25 13:04:11 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| minwt | Integer | ||
| reference | File | ||
| sample_bams | File[] | ||
| matched_control_bams | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| lumpy_prep |
../tools/lumpy_prep.cwl
(CommandLineTool)
|
Perform various functions with samtools to get split reads and discordant reads | |
| delly_calls |
../tools/delly_caller.cwl
(CommandLineTool)
|
Perform SV calling using Delly | |
| lumpy_calls |
../tools/lumpy_caller.cwl
(CommandLineTool)
|
Perform SV calling using Lumpy | |
| wrap_output |
../tools/three_way_merge.cwl
(ExpressionTool)
|
Merge three arrays into an array of arrays, where position i of the output = [array1[i], array2[i], array3[i] | |
| gunzip_manta |
../tools/gunzip.cwl
(CommandLineTool)
|
Unzip a zipped file | |
| manta_caller |
../tools/manta_caller.cwl
(CommandLineTool)
|
Set up and run manta for SV calling | |
| merged_splitters |
../tools/create_array_of_file_arrays.cwl
(ExpressionTool)
|
Merge two arrays into an array of arrays, where position i of the output = [array1[i], array2[i]] | |
| merged_discordant |
../tools/create_array_of_file_arrays.cwl
(ExpressionTool)
|
Merge two arrays into an array of arrays, where position i of the output = [array1[i], array2[i]] | |
| convert_delly_to_vcf |
../tools/bcftovcf.cwl
(CommandLineTool)
|
Convert bcf file to vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| vcf_files | 5d3dbe6e89897ba341f29fd2af26b13e[] |
Permalink:
https://w3id.org/cwl/view/git/656d9ae18f164f983c5672bcf51037cd73309f4f/subworkflows/sv_caller.cwl
