Workflow: qc_workflow.cwl
Fetched 2025-12-16 01:22:02 GMT
Verified with cwltool version 3.1.20230127121939
- 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 |
|---|---|---|---|
| gene_list | File | ||
| run_tools | |||
| title_file | File | ||
| inputs_yaml | File | ||
| standard_bams | File[] | ||
| FP_config_file | File | ||
| pool_a_bed_file | File | ||
| pool_b_bed_file | File | ||
| reference_fasta | String | ||
| coverage_threshold | Integer | ||
| sample_directories | Directory[] | ||
| reference_fasta_fai | String | ||
| marianas_duplex_bams | File[] | ||
| A_on_target_positions | File | ||
| B_on_target_positions | File | ||
| marianas_simplex_bams | File[] | ||
| noise__good_positions_A | File | ||
| marianas_unfiltered_bams | File[] | ||
| waltz__min_mapping_quality | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| waltz_workflow |
../waltz/waltz_workflow_all_bams.cwl
(Workflow)
|
||
| qc_workflow_wo_waltz |
qc_workflow_wo_waltz.cwl
(Workflow)
|
This workflow is intended to be used to test the QC module, without having to run the long waltz step |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| combined_qc | Directory |
Permalink:
https://w3id.org/cwl/view/git/f874bd8a9bb7da9839f0aa6be708d5d16f72945d/workflows/QC/qc_workflow.cwl
