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cwlVersion: v1.1
class: CommandLineTool
inputs:
importScript:
type: File
default:
class: File
location: download_genbank_data/from_genbank_to_fasta_and_yaml.py
inputBinding: {position: 1}
dict:
type: Directory
inputBinding:
prefix: --dict-ontology
position: 2
default:
class: Directory
location: dict_ontology_standardization
existing_metadata_from_nuccore:
type: Directory?
inputBinding:
valueFrom: "--skip-request"
position: 3
outputs:
fasta_and_yaml:
type: Directory
outputBinding:
glob: fasta_and_yaml
metadata_from_nuccore:
type: Directory
outputBinding:
glob: metadata_from_nuccore
accessions:
type: File?
outputBinding:
glob: "*.acc"
missing_terms:
type: File
outputBinding:
glob: missing_terms.tsv
requirements:
InitialWorkDirRequirement:
listing:
- entry: $(inputs.existing_metadata_from_nuccore)
entryname: metadata_from_nuccore
DockerRequirement:
dockerPull: bh20-seq-uploader/import
NetworkAccess:
networkAccess: true
baseCommand: python3
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