Workflow: preprocess_vcf.cwl
Fetched 2023-01-19 15:57:00 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/70b13fe2-f445-4161-834c-3224af99ee50
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/b5471548-df30-4486-92de-b01af90d80e5
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/4246d455-59c2-42cc-81a1-27d772991e4a
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/76e894be-580a-4c9f-9067-dbe5cd04b3c5
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/031a8bbe-617e-4e63-b248-87a3d1c3b968
(ExpressionTool)
|
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| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/ca909fad-e5ec-4c9c-b887-a5195607c81c
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/dcf36217-3da3-4b8e-b9cc-9122bfcfb770
(ExpressionTool)
|
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/cf8fbc64-1bd1-410e-bb13-0c58f47b10c0
(ExpressionTool)
|
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| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/8fae923d-bf68-4a59-ac25-d6528c572cc6
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/21614ef4-d206-4812-b1a3-c9ab46916c8c
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/ad63b2ad-5635-4cf6-be6f-4a17f8664e53
(ExpressionTool)
|
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/d785710f-5986-4a1b-b50b-b5c9cfd2d7ef
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/a4dae70d-08ba-4a7e-8d74-3c53ab9a2be8
(ExpressionTool)
|
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| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/0cc1fef6-f9e5-44e8-af3c-2f4ceb076a0b
(ExpressionTool)
|
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/6de00abb-cb99-4291-a4b0-85972cefa182
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/ad42ab7a8c7e190d5f8615b52278346262256424/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/ad42ab7a8c7e190d5f8615b52278346262256424/preprocess_vcf.cwl
