Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:54:35 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/12cdf774-0a6d-4465-b48f-f56936b0eaa0
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/eaded56e-e375-4fca-8602-b788ba1242a3
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/08147d69-3ea0-4dc2-8a75-0fa26ec11556
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/8cf6019c-30cd-4190-bb7e-9c4505754be1
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/2e716c14-1628-4224-b939-ebda5b8e6a25
(ExpressionTool)
|
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| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/b21817f4-e050-41ad-83c9-ba91cae3a44f
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/ac8bdb0d-7109-42ad-a0f9-56f3b0f626f7
(ExpressionTool)
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/899bdf5c-453d-4d86-8412-9589ffa88e31
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/8ba3ae3e-2ce5-4e3b-b22b-05fbb2ff2353
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/2c573205-a8f4-48b9-a6f3-5beb14ef44c3
(ExpressionTool)
|
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| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/74dbd44a-1027-4332-a536-fdd6d94e91a4
(ExpressionTool)
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/fb55c9f5-0f71-48ca-94df-9622d1dd229b
(ExpressionTool)
|
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| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/72baf2d9-1301-4154-81a1-d5fa43f91ed4
(ExpressionTool)
|
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| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/7d0a84ce-386a-4614-8f14-77fcf93b9f81
(ExpressionTool)
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/8ccc4901-b500-4056-be69-6de45ba156ba
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/c162a19d83f872fe0dc0077e18bef22c99423e4d/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/c162a19d83f872fe0dc0077e18bef22c99423e4d/preprocess_vcf.cwl
