Workflow: samples_fillout_workflow.cwl
Fetched 2023-01-03 21:44:22 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 | cf72a5c5f98a7d7796bf25948c057122[] | ||
| bam_files | File[] | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
samples_fillout_workflow.cwl#gbcms/4f409265-8b14-4476-b101-a57e91fb4126
(CommandLineTool)
|
||
| maf2vcf |
samples_fillout_workflow.cwl#maf2vcf/474580a5-4bc2-4511-a9ca-18421ea305f5
(CommandLineTool)
|
||
| merge_vcfs |
samples_fillout_workflow.cwl#merge_vcfs/60a66533-7de3-486a-bf8f-dd0c25daccde
(CommandLineTool)
|
||
| split_vcf_to_mafs |
samples_fillout_workflow.cwl#split_vcf_to_mafs/ba9d851c-771f-4007-af5e-fe05c35c211f
(CommandLineTool)
|
||
| create_samples_list |
samples_fillout_workflow.cwl#create_samples_list/7750154d-c286-4025-871d-cb25bc8a1e3c
(ExpressionTool)
|
||
| concat_with_comments |
samples_fillout_workflow.cwl#concat_with_comments/74e652ae-b353-43c2-960d-97a8afb7377a
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
samples_fillout_workflow.cwl#fix_labels_and_merge_vcfs/c45ee3bc-f6ae-404f-b054-652d93ff09a4
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77/cwl/samples_fillout_workflow.cwl
