Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:52:49 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/50355326-b29e-47b9-94c5-8502445f4588
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/6c608d96-05bc-401a-9a57-d013096a19a3
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/8bada1af-5d39-47d0-8788-af7e7b0c1a95
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/75dd92e0-4250-470b-a7d0-caf13c3533ff
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/d1b26453-c645-409f-b7cd-eb5cace37781
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/2ce4cbe6-9b8f-4cc2-a87b-18afd26cb8fd
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/6dac8a52-2e1a-4118-ab82-553e1ff23848
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/6779d614-10af-4b8a-b33a-2a2a11f92ea1
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/8892228a-d175-4cc8-99dd-2c79f996cb78
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/5717d547-2cc6-4333-a52d-1e4ac6f303c7
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/79d2393a-0eb1-4a01-90e1-6055f6656725
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/84dceaf6-b149-4f14-9362-4fbd5e3a92ca
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/6e06ffba-02d5-4faf-a57f-3ea7a3ac9fdd
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/11a288cc-0186-4159-a31a-f20e16cb4c77
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/7f471d14-cc82-4b0e-bc16-ed7d1d0d5097
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/f736cf8f663fbba8f1b4158431f2b6a6d88491b4/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/f736cf8f663fbba8f1b4158431f2b6a6d88491b4/preprocess_vcf.cwl
