Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:24:47 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/9283fba1-509e-4bff-8fa0-3dbe9d4a76da
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/b25e8c58-21a9-410b-b1ca-7fa3353e7869
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/92c95db3-a075-4bc6-b407-0cd3f3e3c7a6
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/fa1de473-1a11-42c7-ac04-e73469b82d4e
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/a5f4c0b0-0551-40e0-acc1-d2629b6589e8
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/f1e3a5ac-f5f2-4ae3-96d0-e60dfef724fb
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/40ad2fb0-1d81-4229-8a1b-86ce19966f9e
(ExpressionTool)
|
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/34f89e41-c73c-4b01-8bbf-27c7e56a2237
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/b8f978a3-6fd5-4a4e-8b47-b47c63587202
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/9d6a60ff-ed43-48e1-a620-a329643d5a90
(ExpressionTool)
|
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| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/84096f30-99a0-4c96-be0d-fe5d3b3c87eb
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/32423955-7128-4dd6-aeff-8394a465a56a
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/ef0b9e30-33cb-4fc8-8038-a08553782ed7
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/685f83fa-26ba-4666-9be0-2c649afb0f06
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/90d6517e-254b-46fc-8d75-10b924055d8e
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/96324c1392b6b774498e415346956e77e5d8dd86/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/96324c1392b6b774498e415346956e77e5d8dd86/preprocess_vcf.cwl
