|
1
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "Phenix workflow",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "content_id": null,
|
|
|
10 "id": 0,
|
|
|
11 "input_connections": {},
|
|
|
12 "inputs": [
|
|
|
13 {
|
|
|
14 "description": "",
|
|
|
15 "name": "Reference fasta"
|
|
|
16 }
|
|
|
17 ],
|
|
|
18 "label": null,
|
|
|
19 "name": "Input dataset",
|
|
|
20 "outputs": [],
|
|
|
21 "position": {
|
|
|
22 "left": 200,
|
|
14
|
23 "top": 128
|
|
1
|
24 },
|
|
|
25 "tool_errors": null,
|
|
|
26 "tool_id": null,
|
|
|
27 "tool_state": "{\"name\": \"Reference fasta\"}",
|
|
|
28 "tool_version": null,
|
|
|
29 "type": "data_input",
|
|
14
|
30 "uuid": "2f18889e-5448-460b-8167-e04125fd51cf",
|
|
1
|
31 "workflow_outputs": []
|
|
|
32 },
|
|
|
33 "1": {
|
|
|
34 "annotation": "",
|
|
|
35 "content_id": null,
|
|
|
36 "id": 1,
|
|
|
37 "input_connections": {},
|
|
|
38 "inputs": [
|
|
|
39 {
|
|
|
40 "description": "",
|
|
|
41 "name": "R1 fastq"
|
|
|
42 }
|
|
|
43 ],
|
|
|
44 "label": null,
|
|
|
45 "name": "Input dataset",
|
|
|
46 "outputs": [],
|
|
|
47 "position": {
|
|
14
|
48 "left": 189,
|
|
|
49 "top": 296
|
|
1
|
50 },
|
|
|
51 "tool_errors": null,
|
|
|
52 "tool_id": null,
|
|
|
53 "tool_state": "{\"name\": \"R1 fastq\"}",
|
|
|
54 "tool_version": null,
|
|
|
55 "type": "data_input",
|
|
14
|
56 "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c",
|
|
1
|
57 "workflow_outputs": []
|
|
|
58 },
|
|
|
59 "2": {
|
|
|
60 "annotation": "",
|
|
|
61 "content_id": null,
|
|
|
62 "id": 2,
|
|
|
63 "input_connections": {},
|
|
|
64 "inputs": [
|
|
|
65 {
|
|
|
66 "description": "",
|
|
|
67 "name": "R2 fastqs"
|
|
|
68 }
|
|
|
69 ],
|
|
|
70 "label": null,
|
|
|
71 "name": "Input dataset",
|
|
|
72 "outputs": [],
|
|
|
73 "position": {
|
|
|
74 "left": 211,
|
|
14
|
75 "top": 474
|
|
1
|
76 },
|
|
|
77 "tool_errors": null,
|
|
|
78 "tool_id": null,
|
|
|
79 "tool_state": "{\"name\": \"R2 fastqs\"}",
|
|
|
80 "tool_version": null,
|
|
|
81 "type": "data_input",
|
|
14
|
82 "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25",
|
|
1
|
83 "workflow_outputs": []
|
|
|
84 },
|
|
|
85 "3": {
|
|
|
86 "annotation": "",
|
|
|
87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1",
|
|
|
88 "id": 3,
|
|
|
89 "input_connections": {
|
|
|
90 "fastq_input|fastq_input1": {
|
|
|
91 "id": 1,
|
|
|
92 "output_name": "output"
|
|
|
93 },
|
|
|
94 "fastq_input|fastq_input2": {
|
|
|
95 "id": 2,
|
|
|
96 "output_name": "output"
|
|
|
97 },
|
|
|
98 "reference_source|ref_file": {
|
|
|
99 "id": 0,
|
|
|
100 "output_name": "output"
|
|
|
101 }
|
|
|
102 },
|
|
|
103 "inputs": [],
|
|
|
104 "label": null,
|
|
|
105 "name": "Map with BWA-MEM",
|
|
|
106 "outputs": [
|
|
|
107 {
|
|
|
108 "name": "bam_output",
|
|
|
109 "type": "bam"
|
|
|
110 }
|
|
|
111 ],
|
|
|
112 "position": {
|
|
|
113 "left": 423.5,
|
|
14
|
114 "top": 300
|
|
1
|
115 },
|
|
|
116 "post_job_actions": {
|
|
|
117 "RenameDatasetActionbam_output": {
|
|
|
118 "action_arguments": {
|
|
|
119 "newname": "#{fastq_input1 | basename}.bam"
|
|
|
120 },
|
|
|
121 "action_type": "RenameDatasetAction",
|
|
|
122 "output_name": "bam_output"
|
|
|
123 }
|
|
|
124 },
|
|
|
125 "tool_errors": null,
|
|
|
126 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1",
|
|
|
127 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
|
|
|
128 "tool_version": "0.7.12.1",
|
|
|
129 "type": "tool",
|
|
14
|
130 "uuid": "104fb0fa-de5b-4202-a8c3-2e8f0fa1321d",
|
|
1
|
131 "workflow_outputs": []
|
|
|
132 },
|
|
|
133 "4": {
|
|
|
134 "annotation": "",
|
|
|
135 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
|
|
|
136 "id": 4,
|
|
|
137 "input_connections": {
|
|
|
138 "input_bam": {
|
|
|
139 "id": 3,
|
|
|
140 "output_name": "bam_output"
|
|
|
141 },
|
|
|
142 "ref_file": {
|
|
|
143 "id": 0,
|
|
|
144 "output_name": "output"
|
|
|
145 }
|
|
|
146 },
|
|
|
147 "inputs": [],
|
|
|
148 "label": null,
|
|
|
149 "name": "PHE MPileup",
|
|
|
150 "outputs": [
|
|
|
151 {
|
|
|
152 "name": "outvcf",
|
|
|
153 "type": "vcf"
|
|
|
154 }
|
|
|
155 ],
|
|
|
156 "position": {
|
|
|
157 "left": 634,
|
|
14
|
158 "top": 138
|
|
1
|
159 },
|
|
|
160 "post_job_actions": {
|
|
|
161 "RenameDatasetActionoutvcf": {
|
|
|
162 "action_arguments": {
|
|
|
163 "newname": "#{input_bam | basename}.vcf"
|
|
|
164 },
|
|
|
165 "action_type": "RenameDatasetAction",
|
|
|
166 "output_name": "outvcf"
|
|
|
167 }
|
|
|
168 },
|
|
|
169 "tool_errors": null,
|
|
|
170 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
|
|
|
171 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}",
|
|
|
172 "tool_version": "1.0",
|
|
|
173 "type": "tool",
|
|
14
|
174 "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca",
|
|
1
|
175 "workflow_outputs": []
|
|
|
176 },
|
|
|
177 "5": {
|
|
|
178 "annotation": "",
|
|
|
179 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
|
|
|
180 "id": 5,
|
|
|
181 "input_connections": {
|
|
|
182 "input": {
|
|
|
183 "id": 4,
|
|
|
184 "output_name": "outvcf"
|
|
11
|
185 },
|
|
|
186 "ref_fa": {
|
|
|
187 "id": 0,
|
|
|
188 "output_name": "output"
|
|
1
|
189 }
|
|
|
190 },
|
|
|
191 "inputs": [],
|
|
|
192 "label": null,
|
|
|
193 "name": "Filter VCF",
|
|
|
194 "outputs": [
|
|
|
195 {
|
|
|
196 "name": "output",
|
|
|
197 "type": "vcf"
|
|
|
198 }
|
|
|
199 ],
|
|
|
200 "position": {
|
|
|
201 "left": 747,
|
|
14
|
202 "top": 326
|
|
1
|
203 },
|
|
|
204 "post_job_actions": {
|
|
|
205 "RenameDatasetActionoutput": {
|
|
|
206 "action_arguments": {
|
|
|
207 "newname": "#{input | basename}.filtered.vcf"
|
|
|
208 },
|
|
|
209 "action_type": "RenameDatasetAction",
|
|
|
210 "output_name": "output"
|
|
|
211 }
|
|
|
212 },
|
|
|
213 "tool_errors": null,
|
|
|
214 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
|
|
14
|
215 "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"25\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\"}",
|
|
1
|
216 "tool_version": "1.0",
|
|
|
217 "type": "tool",
|
|
14
|
218 "uuid": "51251f05-75d4-4d89-b757-2248b934d630",
|
|
1
|
219 "workflow_outputs": []
|
|
|
220 }
|
|
|
221 },
|
|
14
|
222 "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf"
|
|
1
|
223 } |
