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readme-genePrediction-workflow.cwl
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readme-genePrediction-workflow.cwl
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#! /usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
inputs:
tree: string[]
organization: string
url_genomic_gff: string[]
url_protein_fasta: string[]
url_cds_fasta: string[]
url_transcript_fasta: string[]
link_to_publication: string
steps:
#step1 create_yml_File
create_readme:
run: create_readme.cwl
in: []
out:
[readme_file]
#step2 write_First_Line
writeFirstLine:
run: writeFirstLine.cwl
in:
readme_file: create_readme/readme_file
organization: organization
out:
[out_readme_file]
#step3 write url - gff
writeURL-gff:
run: writeURL.cwl
in:
readme_file: writeFirstLine/out_readme_file
url: url_genomic_gff
out:
[out_readme_file]
#step4 write url - cds
writeURL-cds:
run: writeURL.cwl
in:
readme_file: writeURL-gff/out_readme_file
url: url_cds_fasta
out:
[out_readme_file]
#step5 write url - transcript
writeURL-transcript:
run: writeURL.cwl
in:
readme_file: writeURL-cds/out_readme_file
url: url_transcript_fasta
out:
[out_readme_file]
#step3 write url - protein
writeURL-protein:
run: writeURL-protein.cwl
scatter: url
in:
readme_file: writeURL-transcript/out_readme_file
url: url_protein_fasta
out:
[out_dummy]
#step4 write Information
writeInfo:
run: writeInfo-genePred.cwl
in:
in_dummy: writeURL-protein/out_dummy
readme_file: writeURL-transcript/out_readme_file
tree: tree
link_to_publication: link_to_publication
out:
[out_readme_file]
#step5 write last line
writeLastLine:
run: writeLastLine-genePred.cwl
in:
readme_file: writeInfo/out_readme_file
out:
[out_readme_file]
outputs:
readme_file:
type: File
outputSource: create_readme/readme_file