Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 21:38:40 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/9cca6761-1c87-4bca-ac06-cff0be0a4697
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/b90ca09a-d8fe-4fe3-9050-cf1fc1036061
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/3f6f21eb-3ab9-4df4-bdc1-9a415313f84d
(ExpressionTool)
|
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| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/67275b88-40b9-4a54-824a-6cc844928104
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/7fef5537-14ca-40d6-9211-5ae3a3309cc1
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/05f7691b-25cf-4ef3-aa4c-03b08f7e5701
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/8c7c35a5-26b3-4e4c-b40f-9d1f68a4875f
(ExpressionTool)
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/8a82c5e2-916f-4564-9a91-b11564e32749
(ExpressionTool)
|
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| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/f911378f-ea65-4632-a661-03b5d83b2d2e
(ExpressionTool)
|
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| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/a988d355-5c89-4be8-aca5-73020a727bcf
(ExpressionTool)
|
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| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/2ed78722-b38d-4119-8b14-c2837f133026
(ExpressionTool)
|
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/b18d7a09-1b0e-4803-abab-d247d336b1a6
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/ddfa463a-2bde-4467-8353-3090e4e6007c
(ExpressionTool)
|
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| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/b34c0dd5-f729-48b2-b4f6-a5d8e09be533
(ExpressionTool)
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/a86de592-df5c-4d7a-8f9b-8534c5530fa4
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/a7d65918c444ee3c99c56bd0f08c2ce670a853ed/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/a7d65918c444ee3c99c56bd0f08c2ce670a853ed/preprocess_vcf.cwl
