Workflow: preprocess_vcf.cwl
Fetched 2024-05-07 03:31:32 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/efa0f575-16b8-41ca-a885-d831a67ee106
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/c0c8ce27-6c7f-4a46-8b4e-bb0d4772d503
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/260a8dab-3769-4ffd-bb88-a098be937e17
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/4c871acf-e273-4fff-bc21-15de0fd231f1
(ExpressionTool)
|
||
| gather_clean_vcfs |
preprocess_vcf.cwl#gather_clean_vcfs/3bfb0456-5226-4e42-bbce-06a8b2ea15d4
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/3df1ee4b-1ed1-4405-b564-6fb06ff54668
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/b1edd624-6564-4a04-bd5c-03fd3e4d58d7
(ExpressionTool)
|
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| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/d57bf258-fa0d-4f8a-b178-15a7272f5d8f
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/0b22cef1-14f7-4458-8eba-36ba86c2d5c8
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/f749075d-d13c-4649-a94c-7d54f0fc85b4
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/b27a677e-d993-451b-a9f2-841130d7a11b
(ExpressionTool)
|
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| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/0a7be2fd-cdff-4574-8fef-61c271c40088
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/cd3ba8ff-d0f0-46f5-9a69-bdd92aac0fce
(ExpressionTool)
|
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| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/cc4deb95-361e-443e-bf55-835c91a0953f
(ExpressionTool)
|
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| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/676cdc91-9ca4-4db2-a005-20c9ce5053ea
(ExpressionTool)
|
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/afe2690f-46b9-4a66-9120-b03bbafdb27e
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/40bf56daf9edab82e0f964dbd6961ca1111cd35f/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/40bf56daf9edab82e0f964dbd6961ca1111cd35f/preprocess_vcf.cwl
