Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:07:30 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/4c50165c-736e-4362-8529-bd2def5f5e15
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/f2cac77c-5487-4f49-bec2-0b612c3aa247
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/aab1ca44-628c-4254-a628-bbe45e97b2c4
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/3e2a69da-15e5-47f0-9be4-cefa5386d2e7
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/350b62e5-fa31-47b5-97eb-4afa4ec54cf4
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/28122081-02c1-4c42-9adc-b40993f625f4
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/5e88cea1-929f-49de-9240-60e60777c51b
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/d1250df1-eec0-4714-8253-289d8c429607
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/e4bdca29-0c36-45ba-8d5e-380f46cb4145
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/a08d39cc-d9bb-4dee-9d6e-b2799e1a5959
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/9597e844-64ef-4b15-bcd8-c69fbc2f1065
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/c9669c0b-0ce7-44ab-9a5a-711018d05d0b
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/16cee563-2257-47fe-be2c-23dd692a23b6
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/b232da4b-1277-4079-a51e-a5dcf742eac8
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/6d2d0ded-e1a3-4228-983e-dc56590419ed
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/1cfe5c41d640b85866f484933b8f9bb4c175796f/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/1cfe5c41d640b85866f484933b8f9bb4c175796f/preprocess_vcf.cwl
