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final_chunking.cwl
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final_chunking.cwl
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class: Workflow
cwlVersion: v1.2
$namespaces:
edam: 'http://edamontology.org/'
s: 'http://schema.org/'
$schemas:
- 'http://edamontology.org/EDAM_1.20.owl'
- 'https://schema.org/version/latest/schemaorg-current-http.rdf'
requirements:
- class: ResourceRequirement
ramMin: 10000
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: ScatterFeatureRequirement
inputs:
fasta: File
ffn: File
faa: File
LSU: File?
SSU: File?
outputs:
nucleotide_fasta_chunks:
type: File[]?
outputSource: chinking_fasta_nucleotide/chunks
protein_fasta_chunks:
type: File[]?
outputSource: chinking_fasta_proteins/chunks
SC_fasta_chunks:
type: File[]?
outputSource: chinking_SC_fasta_nucleotide/chunks
steps:
chinking_fasta_nucleotide:
run: ../../utils/result-file-chunker/result_chunker.cwl
in:
infile:
- fasta
- ffn
format_file: {default: fasta}
outdirname: {default: folder}
type_fasta: {default: n}
out:
- chunks
chinking_fasta_proteins:
run: ../../utils/result-file-chunker/result_chunker.cwl
in:
infile:
source:
- faa
linkMerge: merge_nested
format_file: {default: fasta}
outdirname: {default: folder}
type_fasta: {default: p}
out:
- chunks
chinking_SC_fasta_nucleotide:
when: $(inputs.lsu != null && inputs.ssu != null)
run: ../../utils/result-file-chunker/result_chunker.cwl
in:
lsu: LSU
ssu: SSU
infile:
- LSU
- SSU
format_file: {default: fasta}
outdirname: {default: folder}
type_fasta: {default: n}
out:
- chunks