comparison ngsap-vc/Haplotypecaller.ga @ 3:0d10255b5434 draft default tip

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author scisjnu123
date Thu, 03 Oct 2019 10:42:15 -0400
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2:2c7824a8d764 3:0d10255b5434
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "Haplotypecaller workflow.",
4 "format-version": "0.1",
5 "name": "Haplotypecaller",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Input Dataset"
15 }
16 ],
17 "label": null,
18 "name": "Input dataset",
19 "outputs": [],
20 "position": {
21 "left": 198,
22 "top": 208.1666717529297
23 },
24 "tool_errors": null,
25 "tool_id": null,
26 "tool_state": "{\"name\": \"Input Dataset\"}",
27 "tool_version": null,
28 "type": "data_input",
29 "user_outputs": [],
30 "uuid": "b9fb671f-f07f-498c-8c85-619987501313"
31 },
32 "1": {
33 "annotation": "",
34 "id": 1,
35 "input_connections": {
36 "analysis_type|cond_bam_input|input": {
37 "id": 0,
38 "output_name": "output"
39 }
40 },
41 "inputs": [],
42 "label": null,
43 "name": "GATK",
44 "outputs": [
45 {
46 "name": "rtc_output_intervals",
47 "type": "gatk_interval"
48 },
49 {
50 "name": "ir_output_bam",
51 "type": "bam"
52 },
53 {
54 "name": "br_table",
55 "type": "tabular"
56 },
57 {
58 "name": "ac_plotsReportFile",
59 "type": "pdf"
60 },
61 {
62 "name": "pr_output_bam",
63 "type": "bam"
64 },
65 {
66 "name": "hc_output_gvcf",
67 "type": "vcf"
68 },
69 {
70 "name": "gg_output_gvcf",
71 "type": "vcf"
72 },
73 {
74 "name": "cg_output_vcf",
75 "type": "vcf"
76 },
77 {
78 "name": "cv_output_vcf",
79 "type": "vcf"
80 },
81 {
82 "name": "output_log",
83 "type": "txt"
84 }
85 ],
86 "position": {
87 "left": 484.83331298828125,
88 "top": 200
89 },
90 "post_job_actions": {},
91 "tool_errors": null,
92 "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/gatk/gatk/3.4-0.d9",
93 "tool_state": "{\"__page__\": 0, \"cond_threads\": \"{\\\"cond_threads_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\", \"ref_file\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"\\\"}\", \"__rerun_remap_job_id__\": null, \"cond_BQSR\": \"{\\\"cond_BQSR_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"HaplotypeCaller\\\", \\\"cond_usage\\\": {\\\"emitRefConfidence\\\": \\\"GVCF\\\", \\\"__current_case__\\\": 0, \\\"cond_usage_selector\\\": \\\"GVCF\\\"}, \\\"optional_parameters\\\": {\\\"optional_parameters_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"cond_bam_input\\\": {\\\"input\\\": null, \\\"all_in_one\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 5}\", \"cond_intervals\": \"{\\\"cond_intervals_enabled\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}",
94 "tool_version": "3.4-0.d9",
95 "type": "tool",
96 "user_outputs": [],
97 "uuid": "5988799c-5658-4475-89ee-86f267cfbee1"
98 }
99 },
100 "uuid": "e4f99de3-d6b0-4554-9562-60b2b0eed2d3"
101 }