Workflow: sidearm.cwl
Fetched 2026-06-06 13:19:57 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 |
|---|---|---|---|
| srr | String | ||
| accver | Boolean (Optional) | ||
| prime3 | String (Optional) | ||
| prime5 | String (Optional) | ||
| blastdb | String | ||
| threads | Integer | ||
| nopaired | Boolean | ||
| seqformat | String | ||
| genomefile | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| trim |
trim.cwl
(CommandLineTool)
|
||
| alignsrr |
align_SRR_to_references.cwl
(CommandLineTool)
|
||
| assembly |
assembly.cwl
(CommandLineTool)
|
||
| bam2seqs |
bam2seqs.cwl
(CommandLineTool)
|
||
| summarizebam |
summarize_bam_by_ref.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bamfile | File | ||
| trimlog | File | ||
| trimseqs | File | ||
| report_tsv | File | ||
| assemblylog | File | ||
| viral_contigs | File |
Permalink:
https://w3id.org/cwl/view/git/0c62c1f52cd9530d7a51435dab9e23efe2be96c3/cwl/tools/sidearm.cwl
