Workflow: preprocess_vcf.cwl
Fetched 2023-01-11 22:46:42 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/cf28c3ca-05cd-4ca4-a345-039be21fbe6d
(ExpressionTool)
|
||
| gather_broad_svs |
preprocess_vcf.cwl#gather_broad_svs/0702e9c4-2514-49a8-a0ff-3d3f48a8d4c1
(ExpressionTool)
|
||
| gather_muse_snvs |
preprocess_vcf.cwl#gather_muse_snvs/f8ce200f-9f6b-4b31-b1af-f5d33270e590
(ExpressionTool)
|
||
| gather_broad_snvs |
preprocess_vcf.cwl#gather_broad_snvs/f04b9700-f7de-4484-98a0-3265006141a0
(ExpressionTool)
|
||
| gather_sanger_svs |
preprocess_vcf.cwl#gather_sanger_svs/2aed1d3c-4203-43b6-ac88-4e5ee6b0eabb
(ExpressionTool)
|
||
| gather_sanger_snvs |
preprocess_vcf.cwl#gather_sanger_snvs/9d58f68f-96f1-4eb9-a3c4-e871d0e05a7b
(ExpressionTool)
|
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| gather_broad_indels |
preprocess_vcf.cwl#gather_broad_indels/b34671df-5ad1-4cbb-8486-ab1964366ebe
(ExpressionTool)
|
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| gather_dkfz_embl_svs |
preprocess_vcf.cwl#gather_dkfz_embl_svs/9b0ebd74-bcf5-449e-aeb1-0e3ed1d1365b
(ExpressionTool)
|
||
| gather_sanger_indels |
preprocess_vcf.cwl#gather_sanger_indels/bc8c6af6-e6b8-4677-9c58-dd0411a6397c
(ExpressionTool)
|
||
| gather_smufin_indels |
preprocess_vcf.cwl#gather_smufin_indels/b3ac4f5c-bbcb-4369-9f21-070a5b30dc16
(ExpressionTool)
|
||
| gather_dkfz_embl_snvs |
preprocess_vcf.cwl#gather_dkfz_embl_snvs/c32572f1-e6ad-4595-9272-d55f56127904
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/29701207-b0a6-41b1-baf3-94df79165eb7
(ExpressionTool)
|
||
| gather_dkfz_embl_indels |
preprocess_vcf.cwl#gather_dkfz_embl_indels/6d59bafc-270d-4360-ad4e-f68f30bb7d07
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocess_vcf.cwl#null_filter_extracted_snvs/4ec7ccef-29c2-4b4c-b7d0-835f5fb65c9e
(ExpressionTool)
|
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| gather_muse_snvs_for_cleaning |
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/a63961de-5dd7-4d7b-ade1-afc99330b0c6
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/0fa87c018a21d55cdea6e89be1feec1913144009/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/0fa87c018a21d55cdea6e89be1feec1913144009/preprocess_vcf.cwl
