Workflow: Subworkflow to allow calling cnvkit with cram instead of bam files
Fetched 2023-01-04 17:32:17 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| access | File (Optional) | ||
| method | String (Optional) | ||
| diagram | Boolean (Optional) | ||
| reference | String | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| scatter_plot | Boolean (Optional) | ||
| bait_intervals | File | ||
| drop_low_coverage | Boolean (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_cnvkit |
../tools/cnvkit_batch.cwl
(CommandLineTool)
|
||
| tumor_cram_to_bam |
../tools/cram_to_bam.cwl
(CommandLineTool)
|
samtools view cram to bam | |
| normal_cram_to_bam |
../tools/cram_to_bam.cwl
(CommandLineTool)
|
samtools view cram to bam |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cn_diagram | File (Optional) | ||
| cn_scatter_plot | File (Optional) | ||
| intervals_target | File (Optional) | ||
| reference_coverage | File (Optional) | ||
| intervals_antitarget | File (Optional) | ||
| tumor_target_coverage | File | ||
| normal_target_coverage | File | ||
| tumor_bin_level_ratios | File | ||
| tumor_segmented_ratios | File | ||
| tumor_antitarget_coverage | File | ||
| normal_antitarget_coverage | File |
Permalink:
https://w3id.org/cwl/view/git/9a657bc8c462542dc7f57fba9e04dc1669f966ba/definitions/subworkflows/cram_to_cnvkit.cwl
