Workflow: gatk4_cohort_genotyping.cwl
Fetched 2023-01-04 04:15:21 GMT
Verified with cwltool version 3.1.20221201130942
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- |
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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 |
|---|---|---|---|
| bed_file | File | ||
| job_uuid | String | ||
| reference | File | ||
| gvcf_files | File[] | ||
| thread_count | Integer | ||
| output_prefix | String | ||
| cromwell_engine | Boolean | ||
| number_of_chunks | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| picard_sortvcf |
../../tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
|
||
| gatk3_selectvariants |
../../tools/variant_calling/gatk3_selectvariants.cwl
(CommandLineTool)
|
||
| genomel_pdc_gatk4_cohort_genotyping |
../../tools/variant_calling/genomel_gatk4_cohort_genotyping.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gatk4_cohort_genotyping_vcf | File | ||
| time_metrics_from_picard_sortvcf | File | ||
| time_metrics_from_selectvariants | File | ||
| time_metrics_from_gatk4_cohort_genotyping | File |
Permalink:
https://w3id.org/cwl/view/git/39ddc4b79dc93076787046f591225dc7ca3100ce/genomel/cwl/workflows/variant_calling/gatk4_cohort_genotyping.cwl
