Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:12:32 GMT
Verified with cwltool version 3.1.20221201130942
This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ref | File |
Reference file, used for normalized INDELs |
|
| vcfdir | Directory |
The directory where the files are |
|
| out_dir | String |
The name of the output directory |
|
| filesToPreprocess | String[] |
The files to process |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_for_indel |
preprocess_vcf.cwl#filter_for_indel/df5b6dc0-a103-444b-8b4a-3d9598a7c492
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/22de2a56-9aa3-49d5-85c9-9aa7895c1943
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/2971aa56-3bed-46c5-8a77-dd7b59b5d8ec
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/bbf695d3-0bd4-4e73-9c5d-1f47d9d70234
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/753d8f28-de90-4827-a9a4-1ce24b9ae2e4
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/58b993db-8bd6-46e9-b615-e9aab87e481e
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/5b1e41d1-78d2-489d-8f3e-71a33853306e
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/58d25c59-fe42-485d-afb6-58e2c50699f6
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/28642042-77ea-48ad-aa53-c52ce31c131a
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/816d26f8-53d7-46d8-9b1b-76b207d24f91
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/bbf1017b-00ec-4a77-a29a-dff9b99ae969
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/d0940ce3-d10d-4fa4-8326-a031a0e431b6
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/0d4bb9e2-dffc-4998-b693-39761a6e8c10
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/d6832e8a-7cd4-413a-8593-511f126a64eb
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/2c98634c-73b3-42f8-a2ea-df406cbec572
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/c752ff9f6ad67aa302d793867ba0ea33b85e6bd3/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/c752ff9f6ad67aa302d793867ba0ea33b85e6bd3/preprocess_vcf.cwl
