Workflow: preprocess_vcf.cwl
Fetched 2023-01-12 00:27:00 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/ff2634f4-415c-4916-8414-cb2bbd0488a2
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/1b3d197a-7b44-411c-a31a-dcd3047c80f7
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/0f5786cb-b71c-47f8-932a-1dc86112943d
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/ce7ec6d0-a770-4067-93a6-bb0f14939d01
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/7d38da6d-d240-4e47-979d-6cf56834a8e7
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/c7be757c-1666-47c4-a38f-8540e8b56120
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/b17fbf49-d3ee-4ed6-8da4-a5123de37dcf
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/bea02cbc-ba2e-4fa2-bb2c-2808ee6c431a
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/d71b260d-1e99-4820-92fb-20cf02d5c2ec
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/eecec17f-2273-42e1-8f86-c90770675e41
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/6ce65119-8036-4cd8-9030-1c4047bb8a99
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/d23101ac-a7fa-4ab2-a007-bb682e730977
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/a2c6f34d-262d-4425-867e-84bdf6a75fae
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/3ae34ff5-47f6-4e70-a02c-1a6f9b74b564
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/7f1932c2-2347-4770-9b32-bacdf0151737
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/406343e20d5dd85932e1364f7a29a59e800458e0/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/406343e20d5dd85932e1364f7a29a59e800458e0/preprocess_vcf.cwl
