Workflow: screen out taxa
Fetched 2023-01-14 21:19:46 GMT
Verified with cwltool version 3.1.20221201130942
Remove sequences which align against a reference set using bowtie2. The references are preformatted (index files)
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| jobid | String | ||
| indexDir | Directory | ||
| indexName | String (Optional) | ||
| sequences | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| screen |
../Tools/bowtie2.tool.cwl
(CommandLineTool)
|
organism screening |
Remove sequences from specified host organism using bowtie2: >bowtie2 -f --reorder -p $proc --un $unalignedSequences -x $indexDir/$indexName -U $sequences > /dev/null\" |
| truncate |
../Tools/seqUtil.tool.cwl
(CommandLineTool)
|
seqUtil |
Utility tool for various sequence file transformations. |
| sortInput |
../Tools/seqUtil.tool.cwl
(CommandLineTool)
|
seqUtil |
Utility tool for various sequence file transformations. |
| sortScreenID |
../Tools/seqUtil.tool.cwl
(CommandLineTool)
|
seqUtil |
Utility tool for various sequence file transformations. |
| untruncateScreen |
../Tools/seqUtil.tool.cwl
(CommandLineTool)
|
seqUtil |
Utility tool for various sequence file transformations. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| passed | File |
Permalink:
https://w3id.org/cwl/view/git/9aba38fd1569287b7256ace7163ac84320909f8a/CWL/Workflows/organism-screening.workflow.cwl
