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cwlVersion: v1.1
class: Workflow
inputs:
inputReads: File[]
metadata: File[]
metadataSchema: File
subjects: string[]
outputs:
odgiGraph:
type: File
outputSource: buildGraph/odgiGraph
odgiPNG:
type: File
outputSource: vizGraph/odgiPNG
seqwishGFA:
type: File
outputSource: induceGraph/seqwishGFA
odgiRDF:
type: File
outputSource: odgi2rdf/rdf
readsMergeDedup:
type: File
outputSource: dedup/readsMergeDedup
mergedMetadata:
type: File
outputSource: mergeMetadata/merged
steps:
relabel:
in:
readsFA: inputReads
subjects: subjects
out: [relabeledSeqs, originalLabels]
run: relabel-seqs.cwl
dedup:
in: {readsFA: relabel/relabeledSeqs}
out: [readsMergeDedup, dups]
run: seqkit-rmdup.cwl
overlapReads:
in: {readsFA: dedup/readsMergeDedup}
out: [readsPAF]
run: minimap2.cwl
induceGraph:
in:
readsFA: dedup/readsMergeDedup
readsPAF: overlapReads/readsPAF
out: [seqwishGFA]
run: seqwish.cwl
buildGraph:
in: {inputGFA: induceGraph/seqwishGFA}
out: [odgiGraph]
run: odgi-build.cwl
vizGraph:
in: {inputODGI: buildGraph/odgiGraph}
out: [odgiPNG]
run: odgi-viz.cwl
odgi2rdf:
in: {odgi: buildGraph/odgiGraph}
out: [rdf]
run: odgi_to_rdf.cwl
mergeMetadata:
in:
metadata: metadata
metadataSchema: metadataSchema
subjects: subjects
dups: dedup/dups
originalLabels: relabel/originalLabels
out: [merged]
run: merge-metadata.cwl
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