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cwlVersion: v1.1
class: Workflow
requirements:
SubworkflowFeatureRequirement: {}
inputs:
metadata: File
fasta:
type: File
secondaryFiles: [.fai]
query: string
outputs:
odgiGraph:
type: File
outputSource: make-gfa/odgiGraph
spoaGFA:
type: File
outputSource: make-gfa/spoaGFA
readsMergeDedupSortedByQualAndLen:
type: File
outputSource: make-gfa/readsMergeDedupSortedByQualAndLen
mergedMetadata:
type: File
outputSource: make-gfa/mergedMetadata
steps:
get-subset:
run: from_sparql.cwl
in: {metadata: metadata, query: query, fasta: fasta}
out: [selected]
make-gfa:
run: pangenome-generate_spoa.cwl
in: {metadata: metadata, seqs: get-subset/selected}
out: [odgiGraph, spoaGFA, readsMergeDedupSortedByQualAndLen, mergedMetadata]
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