generated from Sage-Bionetworks/RNASeq-CWLTools
-
Notifications
You must be signed in to change notification settings - Fork 3
/
bam_paired.cwl
274 lines (273 loc) · 7.48 KB
/
bam_paired.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
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
class: Workflow
cwlVersion: v1.0
id: main_paired
label: main-paired
$namespaces:
sbg: 'https://www.sevenbridges.com'
inputs:
- id: cwl_wf_url
type: string
- id: cwl_args_url
type: string
- id: index_synapseid
type: string
- id: synapse_config
type: File
'sbg:x': -522.0704956054688
'sbg:y': -348.93670654296875
- id: synapseid
type: 'string[]'
'sbg:x': -405
'sbg:y': -412
- id: nthreads
type: int
'sbg:x': -422
'sbg:y': -411
- id: genstr
type: string?
- id: output_metrics_filename
type: string?
- id: synapse_parentid
type: string
- id: strand_specificity
type: string?
- id: column_number
type: int?
- id: alignEndsType
type: string?
- id: outFilterMismatchNmax
type: int?
- id: outFilterMultimapScoreRange
type: int?
- id: outFilterMultimapNmax
type: int?
- id: outFilterScoreMinOverLread
type: int?
- id: outFilterMatchNminOverLread
type: int?
- id: outFilterMatchNmin
type: int?
- id: alignSJDBoverhangMin
type: int?
- id: alignIntronMax
type: int?
outputs:
- id: clean_counts
outputSource:
- clean_tables/clean_counts
type: File
- id: clean_log
outputSource:
- clean_tables/clean_log
type: File
- id: clean_metrics
outputSource:
- clean_tables/clean_metrics
type: File
steps:
- id: input_provenance
in:
- id: argurl
source: cwl_args_url
- id: synapseconfig
source: synapse_config
out:
- id: provenance_csv
run: tools/provenance.cwl
label: gather sample provenance
doc: capture the version numbers of input files on Synapse
- id: wf_getindexes
in:
- id: synapseid
source: index_synapseid
- id: synapse_config
source: synapse_config
out:
- id: files
- id: genome_fasta
- id: genemodel_gtf
run: subworkflows/wf-getindexes.cwl
label: Get index files
doc: download the indexed reference genome
- id: wf_alignment
in:
- id: genome_dir
source: wf_getindexes/files
- id: genstr
source: genstr
- id: nthreads
source: nthreads
- id: synapse_config
source: synapse_config
- id: synapseid
source: synapseid
- id: alignEndsType
source: alignEndsType
- id: outFilterMismatchNmax
source: outFilterMismatchNmax
- id: outFilterMultimapScoreRange
source: outFilterMultimapScoreRange
- id: outFilterMultimapNmax
source: outFilterMultimapNmax
- id: outFilterScoreMinOverLread
source: outFilterScoreMinOverLread
- id: outFilterMatchNminOverLread
source: outFilterMatchNminOverLread
- id: outFilterMatchNmin
source: outFilterMatchNmin
- id: alignSJDBoverhangMin
source: alignSJDBoverhangMin
- id: alignIntronMax
source: alignIntronMax
out:
- id: splice_junctions
- id: reads_per_gene
- id: logs
- id: realigned_reads_sam
run: subworkflows/wf-alignment-paired-bam.cwl
label: Alignment sub-workflow
doc: run the alignment sub-workflow
scatter:
- synapseid
scatterMethod: dotproduct
'sbg:x': -310.91680908203125
'sbg:y': -200.39964294433594
- id: wf_buildrefs
in:
- id: genemodel_gtf
source: wf_getindexes/genemodel_gtf
- id: aligned_reads_sam
source: wf_alignment/realigned_reads_sam
valueFrom: $(self[0])
out:
- id: picard_riboints
- id: picard_refflat
run: subworkflows/wf-buildrefs.cwl
label: Reference building sub-workflow
doc: run the subworkflow that builds reference files for picard tools
'sbg:x': -516
'sbg:y': 12
- id: wf_metrics
in:
- id: genome_fasta
source: wf_getindexes/genome_fasta
- id: aligned_reads_sam
source: wf_alignment/realigned_reads_sam
- id: picard_refflat
source: wf_buildrefs/picard_refflat
- id: picard_riboints
source: wf_buildrefs/picard_riboints
- id: basef
source: synapseid
- id: output_metrics_filename
source: output_metrics_filename
- id: strand_specificity
source: strand_specificity
out:
- id: combined_metrics_csv
run: subworkflows/wf-metrics.cwl
label: Metrics sub-workflow
doc: run the metrics subworkflow
scatter:
- aligned_reads_sam
- basef
scatterMethod: dotproduct
'sbg:x': 128
'sbg:y': -185
- id: combine_counts
in:
- id: read_counts
source:
- wf_alignment/reads_per_gene
- id: column_number
source: column_number
out:
- id: combined_counts
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-star/v1.0.0/cwl/combine_counts_study.cwl
label: Combine read counts across samples
doc: combine read counts across all samples
'sbg:x': -63.8984375
'sbg:y': 31.5
- id: combine_metrics
in:
- id: picard_metrics
source:
- wf_metrics/combined_metrics_csv
out:
- id: combined_metrics
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-picardtools/v1.0.1/cwl/combine_metrics_study.cwl
label: Combine Picard metrics across samples
doc: combine picard metrics across all samples
'sbg:x': 343.8936767578125
'sbg:y': -158.5
- id: merge_starlog
in:
- id: logs
source:
- wf_alignment/logs
out:
- id: starlog_merged
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-rnaseq-utils/v1.0.0/cwl/merge_starlog.cwl
label: merge_starlog
doc: merge STAR log files into a single table
'sbg:x': -132.7860107421875
'sbg:y': 294.5
- id: synapse_upload
in:
- id: infiles
source:
- merge_starlog/starlog_merged
- input_provenance/provenance_csv
- combine_counts/combined_counts
- combine_metrics/combined_metrics
- id: synapse_parentid
source: synapse_parentid
- id: synapseconfig
source: synapse_config
- id: argurl
source: cwl_args_url
- id: wfurl
source: cwl_wf_url
out: []
run: tools/upload_synapse.cwl
doc: upload output files to Synapse
- id: clean_tables
in:
- id: count_table
source: combine_counts/combined_counts
- id: star_table
source: merge_starlog/starlog_merged
- id: metric_table
source: combine_metrics/combined_metrics
- id: provenance_csv
source: input_provenance/provenance_csv
out:
- id: clean_counts
- id: clean_log
- id: clean_metrics
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-rnaseq-utils/v1.0.0/cwl/clean_tables.cwl
doc: clean output tables and convert Synapse ID's to specimen ID's
- id: clean_upload
in:
- id: infiles
source:
- clean_tables/clean_counts
- clean_tables/clean_log
- clean_tables/clean_metrics
- id: synapse_parentid
source: synapse_parentid
- id: synapseconfig
source: synapse_config
- id: argurl
source: cwl_args_url
- id: wfurl
source: cwl_wf_url
out: []
run: tools/upload_synapse.cwl
doc: upload the cleaned tables to Synapse
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement