Workflow: genomel_cohort_genotyping.cwl
Fetched 2023-01-12 23:00:51 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 |
|---|---|---|---|
| job_uuid | String | ||
| bam_files | File[] | ||
| 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 | ||
| freebayes_thread_count | Integer | ||
| number_of_chunks_for_gatk | Integer | ||
| gatk4_genotyping_thread_count | Integer | ||
| number_of_chunks_for_freebayes | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort_gatk4 |
cwl/tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
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||
| sort_ensemble |
cwl/tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
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| sort_freebayes |
cwl/tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
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| extract_time_log |
cwl/tools/utils/extract_outputs.cwl
(ExpressionTool)
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| upload_gatk4_vcf |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
|
||
| variant_ensemble |
cwl/tools/variant_calling/vArmyKnife_variant_ensemble.cwl
(CommandLineTool)
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| upload_ensemble_vcf |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
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| upload_freebayes_vcf |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
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| upload_gatk4_vcf_index |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
|
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| gatk4_cohort_genotyping | |||
| upload_ensemble_vcf_index |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
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||
| upload_freebayes_vcf_index |
cwl/tools/utils/awscli_upload.cwl
(CommandLineTool)
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| freebayes_cohort_genotyping |
cwl/workflows/variant_calling/freebayes.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gatk4_vcf | File | ||
| time_logs | File[] | ||
| freebayes_vcf | File | ||
| variant_ensemble_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/7504ead048c3acd64b9b92e44d044d558cb696f2/genomel/genomel_cohort_genotyping.cwl
