Workflow: oxog_varbam_annotate_wf.cwl
This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json `
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
vcfdir | Directory | ||
out_dir | String | ||
refFile | File | ||
tumours | https://w3id.org/cwl/view/git/958b2a392ab2513aa0fbfab558dbf844b549669d/TumourType.yaml#TumourType[] | ||
normalBam | File | ||
refDataDir | Directory | ||
sv-padding | String | ||
minibamName | String | ||
snv-padding | String | ||
indel-padding | String | ||
inputFileDirectory | Directory |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
run_oxog |
oxog_sub_wf.cwl
(Workflow)
|
This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow! |
|
gather_minibams |
oxog_varbam_annotate_wf.cwl#gather_minibams/99ec594e-04e8-4daa-8517-08f44d6c81ae
(ExpressionTool)
|
||
get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/0c37c6c9-5064-427e-a2a0-1384d54d3438
(ExpressionTool)
|
||
preprocess_vcfs |
preprocess_vcf.cwl
(Workflow)
|
This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow. |
|
run_variant_bam |
minibam_sub_wf.cwl
(Workflow)
|
This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow! |
|
filter_merged_sv |
oxog_varbam_annotate_wf.cwl#filter_merged_sv/7117e8d8-b44e-4abc-b6c5-aaf517d2860d
(ExpressionTool)
|
||
get_cleaned_vcfs |
oxog_varbam_annotate_wf.cwl#get_cleaned_vcfs/dd206b4f-b050-47d6-9cfa-9ef3a1f278f0
(ExpressionTool)
|
||
filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/58e1693b-3f1e-4413-bcbd-e66080d8ac95
(ExpressionTool)
|
||
get_extracted_snvs |
oxog_varbam_annotate_wf.cwl#get_extracted_snvs/1cf706d0-c028-4819-976c-417d352a5909
(ExpressionTool)
|
||
filter_merged_indel |
oxog_varbam_annotate_wf.cwl#filter_merged_indel/5af7d1b0-5db3-4922-ab6d-d2f68ca5bd2a
(ExpressionTool)
|
||
flatten_oxog_output |
oxog_varbam_annotate_wf.cwl#flatten_oxog_output/3e864584-8fd6-4f1b-867a-9049b86093ed
(ExpressionTool)
|
||
get_normalized_vcfs |
oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/c87ecaab-09e2-4e07-9f74-fd7ff69be8ad
(ExpressionTool)
|
||
gather_vcfs_for_oxog |
oxog_varbam_annotate_wf.cwl#gather_vcfs_for_oxog/999a9a7c-5bba-4074-a786-cf6120dc27c9
(ExpressionTool)
|
||
run_annotator_indels |
annotator_sub_wf.cwl
(Workflow)
|
This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow! |
|
zip_and_index_files_for_oxog |
zip_and_index_vcf.cwl
(Workflow)
|
This is a very simple workflow of two steps. It will zip an input VCF file and then index it. The zipped file and the index file will be in the workflow output. |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
minibams | File[] |
https://w3id.org/cwl/view/git/958b2a392ab2513aa0fbfab558dbf844b549669d/oxog_varbam_annotate_wf.cwl