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workflow.cwl
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workflow.cwl
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#! /usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
#requirements:
inputs:
scientific_name: string[]
PATH: string[]
tree: string[]
managePy_Path: string
blastdb_Path_production: string[]
hmmerdb_Path_production: string[]
deepPATH_genomic_fasta: string[]
deepPATH_analyses: string[]
genome_fasta_name: string[]
transcript_fasta_name: string[]
cds_fasta_name: string[]
protein_fasta_name: string[]
steps:
#step1 create_yml_File
create_yml:
run: create_yml.cwl
in: []
out:
[Yml_file]
#step2 write_First_Line
writeFirstLine:
run: writeFirstLine.cwl
in:
yml_file: create_yml/Yml_file
out:
[Yml_file]
#step3 edit yml file
writeYml:
run: writeYml.cwl
in:
yml_file: writeFirstLine/Yml_file
scientific_name: scientific_name
PATH: PATH
tree: tree
managePy_Path: managePy_Path
blastdb_Path_production: blastdb_Path_production
hmmerdb_Path_production: hmmerdb_Path_production
deepPATH_genomic_fasta: deepPATH_genomic_fasta
deepPATH_analyses: deepPATH_analyses
genome_fasta_name: genome_fasta_name
transcript_fasta_name: transcript_fasta_name
cds_fasta_name: cds_fasta_name
out:
[Yml_file]
#step4 edit yml file - protein fasta files
writeYml-protein-fasta:
run: writeYml-protein-fasta.cwl
in:
yml_file: writeYml/Yml_file
PATH: PATH
tree: tree
deepPATH_genomic_fasta: deepPATH_genomic_fasta
deepPATH_analyses: deepPATH_analyses
protein_fasta_name: protein_fasta_name
out:
[Yml_file]
outputs:
Yml_file:
type: File
outputSource: create_yml/Yml_file