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amplicon-fasta.workflow.cwl
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amplicon-fasta.workflow.cwl
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cwlVersion: v1.0
class: Workflow
label: rna amplicon analysis for fasta files
doc: RNAs - qc, preprocess, annotation, index, abundance
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
inputs:
jobid: string
sequences: File
filterLn:
type: boolean
default: true
filterAmbig:
type: boolean
default: true
deviation:
type: float
default: 2.0
maxAmbig:
type: int
default: 5
# static DBs
m5nrBDB: File
m5rnaFull: File
m5rnaClust: File
m5rnaIndex: Directory
m5rnaPrefix: string
outputs:
seqStatOut:
type: File
outputSource: qcBasic/seqStatFile
seqBinOut:
type: File
outputSource: qcBasic/seqBinFile
qcStatOut:
type: File
outputSource: qcBasic/qcStatFile
qcSummaryOut:
type: File
outputSource: qcBasic/qcSummaryFile
adapterPassed:
type: File
outputSource: preProcess/trimmed
preProcessPassed:
type: File
outputSource: preProcess/passed
preProcessRemoved:
type: File
outputSource: preProcess/removed
rnaFeatureOut:
type: File
outputSource: annotate/rnaFeatureOut
rnaClustSeqOut:
type: File
outputSource: annotate/rnaClustSeqOut
rnaClustMapOut:
type: File
outputSource: annotate/rnaClustMapOut
rnaSimsOut:
type: File
outputSource: annotate/rnaSimsOut
simSeqOut:
type: File
outputSource: indexSimSeq/simSeqOut
md5ProfileOut:
type: File
outputSource: abundance/md5ProfileOut
lcaProfileOut:
type: File
outputSource: abundance/lcaProfileOut
sourceStatsOut:
type: File
outputSource: abundance/sourceStatsOut
steps:
qcBasic:
run: ../Workflows/qc-basic.workflow.cwl
in:
jobid: jobid
sequences: sequences
kmerLength:
valueFrom: ${ return [6, 15]; }
out: [seqStatFile, seqBinFile, qcStatFile, qcSummaryFile]
preProcess:
run: ../Workflows/preprocess-fasta.workflow.cwl
in:
jobid: jobid
sequences: sequences
stats: qcBasic/seqStatFile
filterLn: filterLn
filterAmbig: filterAmbig
deviation: deviation
maxAmbig: maxAmbig
out: [trimmed, passed, removed]
annotate:
run: ../Workflows/rna-annotation.workflow.cwl
in:
jobid: jobid
sequences: preProcess/passed
m5nrBDB: m5nrBDB
m5rnaFull: m5rnaFull
m5rnaClust: m5rnaClust
m5rnaIndex: m5rnaIndex
m5rnaPrefix: m5rnaPrefix
out: [rnaFeatureOut, rnaClustSeqOut, rnaClustMapOut, rnaSimsOut, rnaFilterOut, rnaExpandOut, rnaLCAOut]
indexSimSeq:
run: ../Workflows/index_sim_seq.workflow.cwl
in:
jobid: jobid
featureSeqs:
source: annotate/rnaFeatureOut
valueFrom: ${ return [self]; }
filterSims:
source: annotate/rnaFilterOut
valueFrom: ${ return [self]; }
clustMaps:
source: annotate/rnaClustMapOut
valueFrom: ${ return [self]; }
out: [simSeqOut, indexOut]
abundance:
run: ../Workflows/abundance.workflow.cwl
in:
jobid: jobid
md5index: indexSimSeq/indexOut
filterSims:
source: annotate/rnaFilterOut
valueFrom: ${ return [self]; }
expandSims:
source: annotate/rnaExpandOut
valueFrom: ${ return [self]; }
lcaAnns:
source: annotate/rnaLCAOut
valueFrom: ${ return [self]; }
clustMaps:
source: annotate/rnaClustMapOut
valueFrom: ${ return [self]; }
out: [md5ProfileOut, lcaProfileOut, sourceStatsOut]