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preprocess-fasta.workflow.cwl
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preprocess-fasta.workflow.cwl
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cwlVersion: v1.0
class: Workflow
label: preprocess fasta
doc: |
Remove reads from fasta files based on sequence stats.
Return fasta files with reads passed and reads removed.
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
jobid: string
sequences: File
stats: File
filterLn:
type: boolean
default: true
filterAmbig:
type: boolean
default: true
deviation:
type: float
default: 2.0
maxAmbig:
type: int
default: 5
outputs:
trimmed:
type: File
outputSource: adapterTrim/outTrim
passed:
type: File
outputSource: filter/passed
removed:
type: File
outputSource: filter/removed
steps:
adapterTrim:
run: ../Tools/autoskewer.tool.cwl
in:
input: sequences
outName:
source: jobid
valueFrom: $(self).080.adapter.trim.passed.fna
out: [outTrim]
filter:
run: ../Tools/filter_fasta.tool.cwl
in:
input: adapterTrim/outTrim
stats: stats
filterLn: filterLn
filterAmbig: filterAmbig
deviation: deviation
maxAmbig: maxAmbig
outPassed:
source: jobid
valueFrom: $(self).100.preprocess.passed.fna
outRemoved:
source: jobid
valueFrom: $(self).100.preprocess.removed.fna
out: [passed, removed]