Workflow: assembly.cwl
Fetched 2023-01-12 11:36:27 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:
BSD 3-clause "New" or "Revised" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fix | String | ||
| minlen | Integer | ||
| prefix | String | ||
| taxons | Integer[] | ||
| leading | Integer | ||
| threads | Integer | ||
| database | Directory | ||
| phredsPe | https://w3id.org/cwl/view/git/66660a64824e4c1019680c6c7ea489ea359cd5f6/Run/assembly-typedef.yml#phred[] | ||
| readsPe1 | File[] | ||
| readsPe2 | File[] | ||
| trailing | Integer | ||
| genomeSize | String | ||
| minReadLen | Integer | ||
| orientation | https://w3id.org/cwl/view/git/66660a64824e4c1019680c6c7ea489ea359cd5f6/Run/assembly-typedef.yml#orientation | ||
| illuminaClip | https://w3id.org/cwl/view/git/66660a64824e4c1019680c6c7ea489ea359cd5f6/Run/assembly-typedef.yml#illuminaClipping (Optional) | ||
| partialMatch | Integer | ||
| pacBioDataDir | Directory | ||
| repeatWorkDir | Directory[] | ||
| slidingWindow | https://w3id.org/cwl/view/git/66660a64824e4c1019680c6c7ea489ea359cd5f6/Run/assembly-typedef.yml#slidingWindow | ||
| noInterspersed | Boolean[] | ||
| repBaseLibrary | File | ||
| diploidOrganism | Boolean | ||
| maxFragmentLens | Integer[] | ||
| noLowComplexity | Boolean[] | ||
| polishedAssembly | String | ||
| corMaxEvidenceErate | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| hdf5check |
hdf5check.cwl
(CommandLineTool)
|
||
| combineCatFiles |
combinecats.cwl
(CommandLineTool)
|
||
| expressionToolBam |
expressiontool.cwl
(ExpressionTool)
|
||
| expressionToolBowtie |
expressiontool.cwl
(ExpressionTool)
|
||
| expressionToolRepeatModeler |
expressiontool.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| deconReport | File | ||
| canuAssembly | File | ||
| trimmedReads | File | ||
| arrowAssembly | File | ||
| pilonAssembly | File | ||
| assemblyMasked | File | ||
| assemblyMerged | File | ||
| correctedReads | File | ||
| contaminatedReads | File | ||
| trimmedReadFiles1 | File[] | ||
| trimmedReadFiles2 | File[] | ||
| deconClassification | File | ||
| decontaminatedReads | File | ||
| sortedBamIndexFileOut | File[] |
Permalink:
https://w3id.org/cwl/view/git/66660a64824e4c1019680c6c7ea489ea359cd5f6/Run/assembly.cwl
