Workflow: SAMSA2 pipeline
Fetched 2023-01-09 00:02:22 GMT
Verified with cwltool version 3.1.20221201130942
SAMSA2 complete workflow for meta-omics read annotation Steps: - Diamond read blastx - Refseq - SEED - SAMSA2 processing
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| step | Integer (Optional) | CWL base step number |
Step number for order of steps |
| threads | Integer (Optional) | number of threads |
number of threads to use for computational processes |
| identifier | String | identifier used |
Identifier for this dataset used in this workflow |
| destination | String (Optional) | Output Destination |
Optional Output destination used for cwl-prov reporting. |
| forward_reads | File | forward reads |
forward sequence file locally |
| reverse_reads | File | reverse reads |
reverse sequence file locally |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| compress_diamond |
../bash/pigz.cwl
(CommandLineTool)
|
compress a file multithreaded with pigz | |
| samsa2_postscripts |
../samsa2/convert.cwl
(CommandLineTool)
|
Samsa2 conversion workflow |
|
| workflow_diamond_seed |
../diamond/diamond.cwl
(CommandLineTool)
|
Diamond workflow implementation |
|
| workflow_diamond_view |
../diamond/view.cwl
(CommandLineTool)
|
Diamond workflow implementation |
|
| samsa2_files_to_folder |
../expressions/files_to_folder.cwl
(ExpressionTool)
|
Transforms the input files to a mentioned directory |
|
| workflow_diamond_refseq |
../diamond/diamond.cwl
(CommandLineTool)
|
Diamond workflow implementation |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| samsa2_output | Directory | SAMSA2 |
functional and classification output folder by samsa2 |
Permalink:
https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_samsa2.cwl
