Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 21:55:36 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/bae4100d-ffc0-4714-9d2b-1f1b7cb0f053
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/03a9655a-093c-45b8-9e27-7d85fc3ce5b4
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/558fa925-9fcb-4c21-abcd-bda2c7114b6c
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/a75d6248-3f0f-45e2-a939-2b0744f7cddf
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/f02b600e-ef74-41fc-9dbe-de905aa47e6d
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/95c1e6ce-4077-4815-a8cf-b32a75c97048
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/87308e80-8529-47d6-ba32-89f289ccdf15
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/d6063a0a-2039-4e32-bd5c-ccc73de78fb0
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/a2be9016-e93a-4cc2-a319-2399101c1b78
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/1667ceba-164f-46b6-81bf-f94e06499a53
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/148e2dcd-20bb-4425-b898-03ee17c442b5
(ExpressionTool)
|
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/cc5070fa-5ade-42d7-a622-dce6fc44a8ae
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/619445db-f9e6-4411-91a2-a16534c44d93
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/cef719b5-0a2a-4d63-9135-a6a27b101806
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/2f02e57a-da49-4a3f-9ad4-06073ff4a59d
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/95da3d32ee8787361333b2eea09afb8f9c3392a9/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/95da3d32ee8787361333b2eea09afb8f9c3392a9/preprocess_vcf.cwl
