CWL Workflow: assembly.cwl

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	String[]
readsPe1	File[]
readsPe2	File[]
trailing	Integer
trueValue	Boolean
falseValue	Boolean
genomeSize	String
minReadLen	Integer
minThreads	Integer
orientation	String
pacBioInBam	Boolean
illuminaClip	https://w3id.org/cwl/view/git/806088a3dfe530cd3c1ce963dfa29556849ac80a/Run/assembly-typedef.yml#illuminaClipping (Optional)
partialMatch	Integer
pacBioDataDir	Directory
slidingWindow	https://w3id.org/cwl/view/git/806088a3dfe530cd3c1ce963dfa29556849ac80a/Run/assembly-typedef.yml#slidingWindow
repBaseLibrary	File
canuConcurrency	Integer
diploidOrganism	Boolean
maxFragmentLens	Integer[]
polishedAssembly	String
corMaxEvidenceErate	Float

ID	Runs	Label	Doc
hdf5check	hdf5check.cwl (CommandLineTool)
combineCatFiles	combinecats.cwl (CommandLineTool)
expressionToolBam	expressiontoolbam.cwl (ExpressionTool)
expressionToolBowtie	expressiontoolbowtie.cwl (ExpressionTool)
expressionToolRepeatModeler	expressiontoolrepeats.cwl (ExpressionTool)

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[]