Workflow: preprocess_vcf.cwl
Fetched 2024-04-23 02:07:52 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/374d0ee7-38cb-430e-8c57-f30cf4dee675
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/6234eaa7-9753-42bb-98b7-6c7584d95330
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/4f39ba5c-09e9-4a03-bb99-4afce94e5607
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/e9ea7170-9f3c-441d-a1e1-491a263361b4
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/65cb870a-cb9d-41d2-b452-9f02069d682a
(ExpressionTool)
|
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| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/915475cd-2a9a-4e83-ae76-d487dd5a810e
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/e6f3a02e-d953-4354-8277-affb3d09be47
(ExpressionTool)
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/93974873-e885-47b3-b1fb-8f9644bf3b8f
(ExpressionTool)
|
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| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/912886ff-0e82-45ba-80b0-4bd609467864
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/e633cc4a-1a96-4c86-95f5-6fd265f7ac32
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/4ef85793-84bd-42b0-a08f-63bbb793a2e6
(ExpressionTool)
|
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/b0e62186-127e-4557-b8e3-7d8b4c15b5f2
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/8c7b91e9-742f-4e72-8f51-a339476b5d23
(ExpressionTool)
|
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| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/85193684-5784-438f-b1ff-75fd3b289ed9
(ExpressionTool)
|
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/87e277d3-3d11-4923-a583-f547fea40730
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/e9f212b6e4c5b8ea691d9112c57201f498cf5dfe/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/e9f212b6e4c5b8ea691d9112c57201f498cf5dfe/preprocess_vcf.cwl
