/
amplicon-wf--v.5-cond.cwl
168 lines (150 loc) · 4.12 KB
/
amplicon-wf--v.5-cond.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
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
requirements:
SubworkflowFeatureRequirement: {}
MultipleInputFeatureRequirement: {}
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
ScatterFeatureRequirement: {}
inputs:
single_reads: File?
forward_reads: File?
reverse_reads: File?
qc_min_length: int
stats_file_name: string
ssu_db:
type: File
secondaryFiles: [ .mscluster ]
lsu_db:
type: File
secondaryFiles: [ .mscluster ]
ssu_tax: string
lsu_tax: string
ssu_otus: string
lsu_otus: string
rfam_models: string[]
rfam_model_clans: string
ssu_label: string
lsu_label: string
5s_pattern: string
5.8s_pattern: string
unite_db: {type: File, secondaryFiles: [.mscluster] }
unite_tax: string
unite_otu_file: string
unite_label: string
itsonedb: {type: File, secondaryFiles: [.mscluster] }
itsonedb_tax: string
itsonedb_otu_file: string
itsonedb_label: string
outputs:
qc-statistics:
type: Directory
outputSource: before-qc/qc-statistics
qc_summary:
type: File
outputSource: before-qc/qc_summary
qc-status:
type: File
outputSource: before-qc/qc-status
hashsum_paired:
type: File[]?
outputSource: before-qc/input_files_hashsum_paired
hashsum_single:
type: File?
outputSource: before-qc/input_files_hashsum_single
fastp_filtering_json_report:
type: File?
outputSource: before-qc/fastp_filtering_json
gz_files:
type: File[]
outputSource: after-qc/gz_files
pickValue: all_non_null
sequence-categorisation_folder:
type: Directory?
outputSource: after-qc/sequence-categorisation_folder
taxonomy-summary_folder:
type: Directory?
outputSource: after-qc/taxonomy-summary_folder
rna-count:
type: File?
outputSource: after-qc/rna-count
ITS-length:
type: File?
outputSource: after-qc/ITS-length
suppressed_upload:
type: Directory?
outputSource: after-qc/suppressed_upload
completed_flag_file:
type: File?
outputSource: touch_file_flag/created_file
no_tax_flag_file:
type: File?
outputSource: after-qc/optional_tax_file_flag
steps:
before-qc:
run: conditionals/amplicon/amplicon-1.cwl
in:
forward_reads: forward_reads
reverse_reads: reverse_reads
single_reads: single_reads
qc_min_length: qc_min_length
stats_file_name: stats_file_name
out:
- filtered_fasta
- qc-statistics
- qc_summary
- qc-status
- input_files_hashsum_paired
- input_files_hashsum_single
- fastp_filtering_json
after-qc:
run: conditionals/amplicon/amplicon-2.cwl
when: $(inputs.status.basename == 'QC-PASSED')
in:
status: before-qc/qc-status
filtered_fasta: before-qc/filtered_fasta
ssu_db: ssu_db
lsu_db: lsu_db
ssu_tax: ssu_tax
lsu_tax: lsu_tax
ssu_otus: ssu_otus
lsu_otus: lsu_otus
rfam_models: rfam_models
rfam_model_clans: rfam_model_clans
ssu_label: ssu_label
lsu_label: lsu_label
5s_pattern: 5s_pattern
5.8s_pattern: 5.8s_pattern
unite_db: unite_db
unite_tax: unite_tax
unite_otu_file: unite_otu_file
unite_label: unite_label
itsonedb: itsonedb
itsonedb_tax: itsonedb_tax
itsonedb_otu_file: itsonedb_otu_file
itsonedb_label: itsonedb_label
out:
- taxonomy-summary_folder
- suppressed_upload
- sequence-categorisation_folder
- rna-count
- gz_files
- ITS-length
- optional_tax_file_flag
touch_file_flag:
when: $(inputs.count != undefined || inputs.status.basename == "QC-FAILED")
run: ../utils/touch_file.cwl
in:
status: before-qc/qc-status
count: after-qc/rna-count
filename: { default: 'wf-completed' }
out: [ created_file ]
$namespaces:
edam: http://edamontology.org/
s: http://schema.org/
$schemas:
- http://edamontology.org/EDAM_1.16.owl
- https://schema.org/version/latest/schemaorg-current-http.rdf
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"