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cwlVersion: v1.1
class: Workflow
requirements:
SubworkflowFeatureRequirement: {}
inputs:
src_project: string
metadataSchema: File
exclude: File?
outputs:
odgiGraph:
type: File
outputSource: pangenome-generate/odgiGraph
# odgiPNG:
# type: File
# outputSource: pangenome-generate/odgiPNG
spoaGFA:
type: File
outputSource: pangenome-generate/spoaGFA
odgiRDF:
type: File
outputSource: pangenome-generate/odgiRDF
readsMergeDedup:
type: File
outputSource: pangenome-generate/readsMergeDedupSortedByQualAndLen
mergedMetadata:
type: File
outputSource: pangenome-generate/mergedMetadata
# indexed_paths:
# type: File
# outputSource: pangenome-generate/indexed_paths
# colinear_components:
# type: Directory
# outputSource: pangenome-generate/colinear_components
steps:
collect-seqs:
run: collect-seqs.cwl
in:
src_project: src_project
schema: metadataSchema
exclude: exclude
out: [relabeledSeqs, mergedMetadata]
pangenome-generate:
run: pangenome-generate_spoa.cwl
in:
seqs: collect-seqs/relabeledSeqs
metadata: collect-seqs/mergedMetadata
exclude: exclude
out: [odgiGraph, spoaGFA, odgiRDF, readsMergeDedupSortedByQualAndLen, mergedMetadata]
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