Workflow: completeWorkflow.cwl
Fetched 2025-04-30 05:04:00 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 |
|---|---|---|---|
| minSize | Integer | ||
| fastqSeqs | https://w3id.org/cwl/view/git/ee872610274d94cfa95ba2a912f01816fe222381/workflows-cwl/readPair.yml#FilePair[] | ||
| fastqMaxEe | Float | ||
| strandInfo | String | ||
| mappingFile | File | ||
| otuRepsetTax | File | ||
| otuTableType | String | ||
| fastqMaxdiffs | Integer | ||
| chimeraFastaDb | File | ||
| otuRepsetFasta | File | ||
| alignmentMethod | String | ||
| chimeraCheckMode | String | ||
| usearchGlobalStrand | String | ||
| assignTaxonomyMethod | String | ||
| assignTaxonomyConfVal | Float | ||
| otuPercentageIdentity | Float | ||
| otuRepsetAlignmentTemplateFasta | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort |
uparseSort.cwl
(CommandLineTool)
|
||
| align |
qiimeAlignSeqs.cwl
(CommandLineTool)
|
||
| derep |
uparseDerepWorkAround.cwl
(CommandLineTool)
|
||
| merge |
uparseFastqMerge.cwl
(CommandLineTool)
|
||
| filter |
uparseFilter.cwl
(CommandLineTool)
|
||
| otuPick |
uparseOTUPick.cwl
(CommandLineTool)
|
||
| underep |
uparseGlobalSearchWorkAround.cwl
(CommandLineTool)
|
||
| renameOTU |
uparseRenameOTUs.cwl
(CommandLineTool)
|
||
| runFastqc |
fastqc.cwl
(CommandLineTool)
|
||
| concatFasta |
concatFasta.cwl
(CommandLineTool)
|
||
| chimeraCheck |
uparseChimeraCheck.cwl
(CommandLineTool)
|
||
| uparseRename |
uparseRenameWithMetadata.cwl
(Workflow)
|
||
| makePhylogeny |
qiimeMakePhylogeny.cwl
(CommandLineTool)
|
||
| uparseUCtoTab |
uparseOtuToTab.cwl
(CommandLineTool)
|
||
| assignTaxonomy |
qiimeAssignTaxonomy.cwl
(CommandLineTool)
|
||
| otuTableToBiom |
qiimeOtusTxt2Biom.cwl
(CommandLineTool)
|
||
| filterAlignment |
qiimeFilterAlign.cwl
(CommandLineTool)
|
||
| generateRReports |
generateRReports.cwl
(CommandLineTool)
|
||
| addTaxonomyToBiom |
qiimeAddMetadata.cwl
(CommandLineTool)
|
||
| createSummaryQualitative |
qiimeSummaryQualitative.cwl
(CommandLineTool)
|
||
| createSummaryObservations |
qiimeSummaryObservations.cwl
(CommandLineTool)
|
||
| arrayOfFilePairsToFileArray |
completeWorkflow.cwl#arrayOfFilePairsToFileArray/41ab91df-7db4-48be-b227-ef3d486ab643
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| reports | Directory[] | ||
| rReports | File[] | ||
| otuBiomFile | File | ||
| otuTreeFile | File | ||
| mergedFastQs | File[] | ||
| otuFastaFile | File | ||
| otuTableFile | File | ||
| ucTabbedFile | File | ||
| derepFastaFile | File | ||
| concatFastaFile | File | ||
| otuTaxonomyFile | File | ||
| sortedFastaFile | File | ||
| renamedFastqFile | https://w3id.org/cwl/view/git/ee872610274d94cfa95ba2a912f01816fe222381/workflows-cwl/readPair.yml#FilePair[] | ||
| filteredFastaFiles | File[] | ||
| noChimeraFastaFile | File | ||
| otuAlignedFastaFile | File | ||
| otuBiomTaxonomyFile | File | ||
| renamedOTUFastaFile | File | ||
| otuSummaryQualitativeFile | File | ||
| otuSummaryeObservationsFile | File | ||
| otuFilteredAlignmentFastaFile | File |
Permalink:
https://w3id.org/cwl/view/git/ee872610274d94cfa95ba2a912f01816fe222381/workflows-cwl/completeWorkflow.cwl
