/
MoveData-workflow.cwl
executable file
·126 lines (122 loc) · 3.76 KB
/
MoveData-workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: InlineJavascriptRequirement
inputs:
PATH: string[]
tree: string[]
scientific_name: string[]
deepPATH_apollo2_data: string[]
deepPATH_bigwig: string[]
deepPATH_genomic_fasta: string[]
deepPATH_analyses: string[]
host_production: string[]
login_apollo2_production: string[]
Apollo_account: string
Gmod_account: string
Gmod_stage_account: string
genome_fasta_name: string[]
transcript_fasta_name: string[]
cds_fasta_name: string[]
protein_fasta_name: string[]
managePy_Path: string
blastdb_Path_production: string[]
hmmerdb_Path_production: string[]
steps:
#step1 create folders on apollo production server
createFolder:
run: files_4_Apollo2Server/MoveData/createFolder.cwl
in:
Apollo_account: Apollo_account
PATH: PATH
tree: tree
deepPATH_bigwig: deepPATH_bigwig
out: [out_dummy]
#step2 transfer folder bigwig to apollo production server
dataTransfer-bigwig:
run: files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl
in:
Apollo_account: Apollo_account
PATH: PATH
tree: tree
deepPATH_bigwig: deepPATH_bigwig
in_dummy: createFolder/out_dummy
out: [out_dummy]
#step3 transfer folder jbrowse to apollo production server
dataTransfer-jbrowse:
run: files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl
in:
Apollo_account: Apollo_account
PATH: PATH
tree: tree
in_dummy: dataTransfer-bigwig/out_dummy
out: [out_dummy]
#step4 transfer folder blat to apollo production server
dataTransfer-blat:
run: files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl
in:
Apollo_account: Apollo_account
PATH: PATH
tree: tree
in_dummy: dataTransfer-jbrowse/out_dummy
out: [out_dummy]
#step5 create folders on gmod production server
createFolder-2gmodProd:
run: files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl
in:
Gmod_account: Gmod_account
PATH: PATH
tree: tree
out: [out_dummy]
#step6 transfer scaffold to gmod production server
dataTransfer-scaffold-2gmodProd:
run: files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl
in:
Gmod_account: Gmod_account
PATH: PATH
tree: tree
deepPATH_genomic_fasta: deepPATH_genomic_fasta
in_dummy: createFolder-2gmodProd/out_dummy
out: [out_dummy]
#step7 create folders on gmod stage server
createFolder-2gmodStage:
run: files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl
in:
Gmod_account: Gmod_stage_account
PATH: PATH
tree: tree
out: [out_dummy]
#step8 transfer scaffold to gmod stage server
dataTransfer-scaffold-2gmodStage:
run: files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl
in:
Gmod_account: Gmod_stage_account
PATH: PATH
tree: tree
deepPATH_genomic_fasta: deepPATH_genomic_fasta
in_dummy: createFolder-2gmodStage/out_dummy
out: [out_dummy]
#Step9 create yml file
create_ymlFile:
run: flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl
in:
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
protein_fasta_name: protein_fasta_name
out: [Yml_file]
outputs:
Yml_file:
type: File
outputSource: create_ymlFile/Yml_file