Workflow: genomel_cohort_gatk4.cwl
Fetched 2023-01-03 21:53:09 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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- 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 |
|---|---|---|---|
| job_uuid | String | ||
| bed_files | File[] | ||
| reference | File | ||
| aws_config | File | ||
| gvcf_files | File[] | ||
| cromwell_engine | Boolean | ||
| upload_s3_bucket | String | ||
| upload_s3_profile | String | ||
| upload_s3_endpoint | String | ||
| aws_shared_credentials | File | ||
| number_of_chunks_for_gatk | Integer | ||
| gatk4_genotyping_thread_count | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort_gatk4 |
cwl/tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
|
||
| extract_time_log |
cwl/tools/utils/extract_outputs.cwl
(ExpressionTool)
|
||
| upload_gatk4_vcf |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
|
||
| upload_gatk4_vcf_index |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
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| gatk4_cohort_genotyping |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gatk4_vcf | File | ||
| time_logs | File[] |
Permalink:
https://w3id.org/cwl/view/git/7f01768479e6a77a5caf6b3382174aa038ba05fc/genomel/genomel_cohort_gatk4.cwl
