/
MoveData-workflow.cwl
executable file
·136 lines (132 loc) · 4.11 KB
/
MoveData-workflow.cwl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
#!/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 transfer scaffold to apollo production server
dataTransfer-scaffold-2apollo:
run: files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl
in:
Apollo_account: Apollo_account
PATH: PATH
tree: tree
deepPATH_genomic_fasta: deepPATH_genomic_fasta
in_dummy: dataTransfer-blat/out_dummy
out: [out_dummy]
#step6 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]
#step7 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]
#step8 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]
#step9 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]
#Step10 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