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viral_annotation_swf.cwl
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viral_annotation_swf.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
label: ViPhOG annotations
requirements:
ScatterFeatureRequirement: {}
inputs:
input_fastas:
type:
type: array
items: ["File", "null"]
doc: |
FASTA Protein files
hmmer_table:
type: File
doc: |
HMMER concatenated tsv
steps:
viral_annotation:
run: viral_annotation.cwl
scatter: input_fasta
label: contigs annotation
in:
input_fasta: input_fastas
input_table: hmmer_table
out:
- annotation_table
outputs:
annotation_tables:
outputSource: viral_annotation/annotation_table
type: File[]
doc: |
"Run viral_contigs_annotation.py on an array of files"
$namespaces:
edam: http://edamontology.org/
s: http://schema.org/
$schemas:
- http://edamontology.org/EDAM_1.16.owl
- https://schema.org/version/latest/schemaorg-current-http.rdf
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder:
- class: s:Organization
s:name: "EMBL - European Bioinformatics Institute"
s:url: "https://www.ebi.ac.uk"