Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:10:16 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/1b1c8ec9-2074-4c59-b6cf-d9a1d2cfb48b
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/b95775db-f181-4eab-99c9-3e43402f0a99
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/43c22c7c-7be5-4e3f-97df-847ae449b88e
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/ea1d515f-7873-43d7-b25d-979a6b3801d5
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/7bc6ed74-a0ed-4198-9999-3316efc3f673
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/c226c9a9-ee36-4bb4-b394-e20809ce0c8e
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/3071a7fc-0ca7-4b69-bebb-9a10057de5b5
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/5988b86f-75cf-46a3-baaf-15e5689e339d
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/646ffa4d-b9e2-4279-891b-b0e5aebae7fd
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/b6794590-0798-449c-9f17-b96acaf2d408
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/5ba1d083-b23f-40ca-9438-2faa6bba6f30
(ExpressionTool)
|
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/ce9933fa-c8f0-48d2-8936-6a40e2598e07
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/02c6b54a-8e6d-4626-bd17-68093c973559
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/3a89c54c-4ccf-4975-ac4d-d38330b82f45
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/3bb28fd9-b0af-4b8e-8944-988571338e2a
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/3bd1b85615fcae5092ccacce2eac395b9a6f1950/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/3bd1b85615fcae5092ccacce2eac395b9a6f1950/preprocess_vcf.cwl
