Workflow: alignment_prep.cwl
Fetched 2023-01-15 00:45:48 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:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| job_uuid | String | ||
| input_bam | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bam_to_fastq |
../../tools/harmonization/bam_to_fastq.cwl
(CommandLineTool)
|
||
| get_readgroup_info |
../../tools/harmonization/get_readgroup_name.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_fastq1 | File[] | ||
| output_fastq2 | File[] | ||
| output_readgroup_lines | String[] | ||
| output_readgroup_names | String[] | ||
| time_metrics_from_bam_to_fastq | File |
Permalink:
https://w3id.org/cwl/view/git/f55f0011de7db66f873ffb0f700f3fe26b33911e/genomel/cwl/workflows/harmonization/alignment_prep.cwl
