Workflow: samples_fillout_workflow.cwl
Fetched 2023-01-09 18:13:31 GMT
Verified with cwltool version 3.1.20221201130942
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| samples | c63b57ae9a51b7771c97a6daf23dd3c6[] | ||
| bam_files | File[] | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
samples_fillout_workflow.cwl#gbcms/fe645b6f-1e52-46b4-a7aa-028a0db7734d
(CommandLineTool)
|
||
| maf2vcf |
samples_fillout_workflow.cwl#maf2vcf/b258e53e-ce00-4ea1-b1c2-db022809aabb
(CommandLineTool)
|
||
| merge_vcfs |
samples_fillout_workflow.cwl#merge_vcfs/ac547816-04d4-4c9c-ad41-64cec16543e1
(CommandLineTool)
|
||
| split_vcf_to_mafs |
samples_fillout_workflow.cwl#split_vcf_to_mafs/0b9f0f66-3abd-46fe-b993-199aa45cb108
(CommandLineTool)
|
||
| create_samples_list |
samples_fillout_workflow.cwl#create_samples_list/96c09151-7b79-4b90-b6df-efc6ffb71c2b
(ExpressionTool)
|
||
| concat_with_comments |
samples_fillout_workflow.cwl#concat_with_comments/45fe77b5-611d-4171-bbf4-edc4e8a8892b
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
samples_fillout_workflow.cwl#fix_labels_and_merge_vcfs/dcdc34a1-1949-4376-9581-22ed8192aef6
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e/cwl/samples_fillout_workflow.cwl
