Workflow: genomel_cohort_freebayes.cwl
Fetched 2026-05-31 16:16:19 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:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File | ||
| job_uuid | String | ||
| bed_files | File[] | ||
| reference | File | ||
| aws_config | File | ||
| cromwell_engine | Boolean | ||
| upload_s3_bucket | String | ||
| upload_s3_profile | String | ||
| upload_s3_endpoint | String | ||
| aws_shared_credentials | File | ||
| freebayes_thread_count | Integer | ||
| number_of_chunks_for_freebayes | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort_freebayes |
cwl/tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
|
||
| extract_time_log |
cwl/tools/utils/extract_outputs.cwl
(ExpressionTool)
|
||
| merge_passed_bed |
cwl/tools/utils/merge_files.cwl
(CommandLineTool)
|
||
| upload_passed_bed |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
|
||
| upload_freebayes_vcf |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
|
||
| upload_freebayes_vcf_index |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
|
||
| freebayes_cohort_genotyping |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| time_logs | File[] | ||
| passed_bed | File | ||
| freebayes_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/3b9d07ff1dd10e323fbba33026b888b3a269136b/genomel/genomel_cohort_freebayes.cwl
