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CompPASS-Plus_workflow.cwl
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CompPASS-Plus_workflow.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
inputs:
CompPASS_pre_R : File
id_remapper_py: File
CompPASS_R : File
protein_directory_path: string
from:
type: string
default: "ACC"
to:
type: string
default: "GENENAME"
remapped_identifiers:
type: string
default: "remapped_identifiers.csv"
email:
type: string
default: "charlotte.adams@student.uantwerpen.be"
fileType:
type: string
default: "CSV"
outputs:
CompPASS_csv:
type: File
outputSource: CompPASS/CompPASS_csv
steps:
CompPASS_pre:
run: Tools/CompPASS_pre.cwl
in:
CompPASS_pre_R: CompPASS_pre_R
protein_directory_path: protein_directory_path
out:
[protein_accessions_csv]
id_remapper:
run: Tools/id_remapper.cwl
in:
id_remapper_py: id_remapper_py
protein_accessions_csv: CompPASS_pre/protein_accessions_csv
from: from
to: to
remapped_identifiers: remapped_identifiers
email: email
fileType: fileType
out:
[remapped_identifiers_csv]
CompPASS:
run: Tools/CompPASS.cwl
in:
CompPASS_R: CompPASS_R
protein_directory_path: protein_directory_path
gene_names: id_remapper/remapped_identifiers_csv
out:
[CompPASS_csv]