Workflow: aws_freebayes.cwl
Fetched 2023-01-04 21:05:04 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File | ||
| bed_file | File | ||
| job_uuid | String | ||
| reference | File | ||
| thread_count | Integer | ||
| output_prefix | String | ||
| number_of_chunks | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| aws_freebayes |
../../tools/variant_calling/aws_freebayes.cwl
(CommandLineTool)
|
||
| picard_sortvcf |
../../tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
|
||
| extract_pass_pair |
../../tools/utils/extract_pass_pair.cwl
(CommandLineTool)
|
||
| gatk3_selectvariants |
../../tools/variant_calling/gatk3_selectvariants.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| log_file | File | ||
| passed_bed | File[] | ||
| freebayes_vcf | File | ||
| time_metrics_from_freebayes | File | ||
| time_metrics_from_picard_sortvcf | File | ||
| time_metrics_from_selectvariants | File |
Permalink:
https://w3id.org/cwl/view/git/28bb82ba031041321ff9caa5c299ec1bb15d7471/genomel/cwl/workflows/variant_calling/aws_freebayes.cwl
