Workflow: waltz-workflow.cwl
Fetched 2024-04-19 17:18:50 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bed_file | File | ||
| gene_list | File | ||
| input_bam | File | ||
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools | ||
| waltz__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/waltz.yaml#waltz__params | ||
| reference_fasta | String | ||
| reference_fasta_fai | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| count_reads |
../../cwl_tools/waltz/CountReads.cwl
(CommandLineTool)
|
None |
|
| pileup_metrics |
../../cwl_tools/waltz/PileupMetrics.cwl
(CommandLineTool)
|
||
| grouped_waltz_files |
../../cwl_tools/expression_tools/group_waltz_files.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| pileup | File | ||
| waltz_output_files | File[] |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/waltz/waltz-workflow.cwl
