Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:05:34 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/f8b124be-e8c2-48ed-bc66-57329c12ece5
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/480b614f-e923-4897-8489-e3a74d860685
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/3fd5c6bc-104e-497b-995c-ae49b38d50b6
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/71df0a60-987a-4ecd-8d8e-4eb9795b41d8
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/f827e20f-ff0d-4d2f-8672-c7338c9bb1d7
(ExpressionTool)
|
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| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/2cb2b0b9-61e9-42db-9fe3-3351cba1f174
(ExpressionTool)
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| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/d648e664-ff71-45b7-9a8f-7af7e23017b3
(ExpressionTool)
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/2690c02b-ad9b-4c79-9c37-6d24e297a590
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/41268fbf-0f1d-46ef-96b8-823e5b493f22
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/66f8090e-eba8-4c0c-b095-d514b950a2a1
(ExpressionTool)
|
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| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/30b0a4bd-008f-4a6a-bd49-f6408d329af0
(ExpressionTool)
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/6b232753-7624-4027-852e-c7bc0085d67b
(ExpressionTool)
|
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| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/2bc43113-e131-4623-9578-55cb5fc540c7
(ExpressionTool)
|
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| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/006dcf61-c1b8-4754-8080-2d02d39928b6
(ExpressionTool)
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/de1b5c00-c00e-4739-ac82-b877f7a1f025
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/958b2a392ab2513aa0fbfab558dbf844b549669d/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/958b2a392ab2513aa0fbfab558dbf844b549669d/preprocess_vcf.cwl
