Workflow: manta.cwl
Fetched 2024-06-10 23:59:41 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| version | String | ||
| ref_fasta | File | ||
| project_name | String | ||
| sv_run_tools | https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/resources/schemas/sv_tools.yaml#sv_run_tools | ||
| sv_sample_id | String[] | ||
| sv_normal_bam | File | ||
| sv_tumor_bams | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| manta |
../../cwl_tools/manta/manta.cwl
(CommandLineTool)
|
||
| index_tumor |
../../cwl_tools/samtools/index.cwl
(CommandLineTool)
|
||
| index_normal |
../../cwl_tools/samtools/index.cwl
(CommandLineTool)
|
||
| annotate_manta |
../../cwl_tools/manta/manta_annotation.cwl
(CommandLineTool)
|
||
| combine_sv_vcfs |
../../cwl_tools/manta/manta_concat.cwl
(CommandLineTool)
|
||
| filter_tumor_reads_ending_in_indels |
../../cwl_tools/manta/manta_filter.cwl
(CommandLineTool)
|
The purpose of this step is to filter out reads from bams that have terminating INDELs. These reads are a new development since upgrading to Abra2, and are not supported by Manta. |
|
| filter_normal_reads_ending_in_indels |
../../cwl_tools/manta/manta_filter.cwl
(CommandLineTool)
|
The purpose of this step is to filter out reads from bams that have terminating INDELs. These reads are a new development since upgrading to Abra2, and are not supported by Manta. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| sv_directory | Directory[] | ||
| concatenated_vcf | File | ||
| annotated_sv_file | File[] |
Permalink:
https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/workflows/subworkflows/manta.cwl
