Workflow: preprocess_vcf.cwl
Fetched 2024-11-27 08:20:19 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/06d3dcbf-a739-4d63-83aa-7d164374994b
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/0fb678d9-b5bd-4fa0-bf2b-f40a058b2e93
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/04fb4a93-bb3e-4ea9-b110-c53c62900aa1
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/c76184da-8bef-4242-8be7-081bcec2b1cc
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/e262f8e3-c8c7-4e67-9350-951565dcb0f6
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/f4733704-627b-46d0-ba37-fe2884fe706d
(ExpressionTool)
|
||
| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/e6780621-6dbc-4af1-804a-58093ffe48df
(ExpressionTool)
|
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/7c7e7a3f-bb85-4f08-bc71-bb62ea86c48e
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/9209f9b7-5491-44f7-8d34-97b63024104b
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/712cf199-bc2f-4c2c-974f-6bbda6b2f953
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/67c72323-52fd-4bd9-8235-8286fb9a676b
(ExpressionTool)
|
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| populate_output_record |
preprocess_vcf.cwl#populate_output_record/2d672c5e-975c-4160-9bbe-dd8d5af7e439
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/bfe8bbf9-2cd7-4205-9d2f-c55f79646164
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/6d458453-82a7-4485-a63e-a12fd93e14b9
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/cccdae23-345e-4397-9d36-7d54a4623908
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/e9f3694e31e3c1570183a4f444a44015766f9f2f/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/e9f3694e31e3c1570183a4f444a44015766f9f2f/preprocess_vcf.cwl
