- 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