Workflow: fastqtosam_pe.cwl
Fetched 2023-01-12 16:30:44 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 |
|---|---|---|---|
| bioclient_config | File | ||
| readgroup_fastq_pe | https://w3id.org/cwl/view/git/a3eec6c1081d28efe00a0d269fb41303acc4ccdd/tools/readgroup_no_pu.yaml#readgroup_fastq_pe |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| emit_pu |
../../tools/fastq-to-sam-pu.cwl
(CommandLineTool)
|
||
| picard_fastqtosam_pe |
../../tools/picard_fastqtosam_pe.cwl
(CommandLineTool)
|
||
| extract_forward_fastq |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_reverse_fastq |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_bam | File |
Permalink:
https://w3id.org/cwl/view/git/a3eec6c1081d28efe00a0d269fb41303acc4ccdd/workflows/fastqtosam/fastqtosam_pe.cwl
