Workflow: preprocess_vcf.cwl
Fetched 2024-11-24 04:43:06 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/a77441f3-25cc-4349-b58f-90c181764275
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/72c73ea3-e85e-474a-9dde-2fc46617cb6a
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/eb577ae5-be16-49cd-80b5-87b0ae93f754
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/fac4cbdb-b775-4ce8-b9e4-12e90742adc7
(ExpressionTool)
|
||
| gather_clean_vcfs |
preprocess_vcf.cwl#gather_clean_vcfs/f70c2cce-29c6-4b4d-9d33-d5f63f433377
(ExpressionTool)
|
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| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/e04241cd-24bd-4095-8799-ad91fd66a557
(ExpressionTool)
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| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/6303840b-20fd-471b-925a-08898adf8cc1
(ExpressionTool)
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| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/350c473f-a93e-4e68-a6b9-de6fe987ef55
(ExpressionTool)
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/bea37fe4-7c75-41e3-84f3-aa4b864f0697
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/77b5da08-2eb9-4ff7-bf3e-e8f4e3fae868
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/9444ca22-c4b7-46b2-9e7a-1f36faf44934
(ExpressionTool)
|
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| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/f633b1ee-f835-4510-a849-2f02453f0197
(ExpressionTool)
|
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/b24aa4d9-1b75-4b86-b796-79ce1d204064
(ExpressionTool)
|
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| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/5184e0da-8579-492e-978e-44f5e1815d89
(ExpressionTool)
|
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| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/2967391e-39f2-4ccb-ac63-b40dd41319f1
(ExpressionTool)
|
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/7abbb6b1-2bd5-44ff-aff5-ec36584edb69
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/6366ed398da10019b6d81a789291af6d909f28f4/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/6366ed398da10019b6d81a789291af6d909f28f4/preprocess_vcf.cwl
