Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 21:39:32 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 | ||
| vcfdir | Directory | ||
| out_dir | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter |
preprocess_vcf.cwl#filter/c8bdca13-b8c7-4d96-9b84-6e658ef79f32
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/f317f788-4422-4397-a032-99dbc641cf42
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/e41be5b7-9d5a-4f75-a01d-160f77f8c7a9
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/603c9c56-ba00-4707-8f08-ae290fa97ab0
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/7996c694-f028-4ee7-9931-174d2168249b
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/90a1ed2b-7ff8-41c3-9e34-f98da2a8ad30
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/a0a085c0-5e40-40d0-8841-1f66f059e2ea
(ExpressionTool)
|
||
| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/e300c533-c7f8-4ea0-9cbe-dc53a76a1370
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/8d4b7eec-9d04-41b4-8a35-3028ef15f258
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/c24a15d0-844a-4b0b-972d-7d74937587d0
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/70650c4a-385b-476b-94c1-17f3b2a63773
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/49f61446-48af-4fdc-b59f-08c874418d1a
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/54b89845-1912-4d3f-b430-0be74bb79435
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/69dabdde-2667-4b6a-b146-d846591bb768
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/88c5eef2f5ee5c1e878b0476f6e1f74cecf9ec29/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/88c5eef2f5ee5c1e878b0476f6e1f74cecf9ec29/preprocess_vcf.cwl
