Mercurial > repos > elixir-it > mutect2

comparison GDC-DNA-Seq-pipeline-galaxy-wrapper.git @ 3:63456e69f310 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Thu, 28 Jun 2018 06:26:18 -0400
parents
children
comparison
equal deleted inserted replaced
2:1f25d6323970 3:63456e69f310
1
2
3
4
5
6
7 <!DOCTYPE html>
8 <html lang="en">
9 <head>
10 <meta charset="utf-8">
11 <link rel="dns-prefetch" href="https://assets-cdn.github.com">
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/">
18
19
20
21 <link crossorigin="anonymous" media="all" integrity="sha512-pCRDtdb3GlUU48h+oRJVA8f0GddrLnU97wB7mHQ7q6c40vMbMMZsFdk0IMhkUFRqw1M/y4EkWxtaKwfeFezOkQ==" rel="stylesheet" href="https://assets-cdn.github.com/assets/frameworks-73f533b7cc08a9d040e601cfd38fa585.css" />
22 <link crossorigin="anonymous" media="all" integrity="sha512-pscKt6TONS3P9zPqdDjngC5prTq2tL4UT8MfWSiqhftwRK8aipsxEuebGlIpobamrDHDV//uvSMkcPXLduUrWw==" rel="stylesheet" href="https://assets-cdn.github.com/assets/github-a0a727fb61e0eacfb1f33d2f365272f8.css" />
23
24
25 <link crossorigin="anonymous" media="all" integrity="sha512-YBQhG++AtbZ1OJfwAkSqS9GCbbYzicxNDYKdMaLTV49eF0Lks0Bs9Egbu46uQi62AyUInQS8Cx6GGkK6uZnqFQ==" rel="stylesheet" href="https://assets-cdn.github.com/assets/site-14cf418638c848dd5bbac72b6f77dfa2.css" />
26
27
28 <meta name="viewport" content="width=device-width">
29
30 <title>GitHub - Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper: galaxy wrappers GDC-DNA-Seq-pipeline</title>
31 <meta name="description" content="GitHub is where people build software. More than 28 million people use GitHub to discover, fork, and contribute to over 85 million projects.">
32 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
33 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
34 <meta property="fb:app_id" content="1401488693436528">
35
36
37 <meta property="og:image" content="https://avatars2.githubusercontent.com/u/39985517?s=400&amp;v=4" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta property="og:url" content="https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta property="og:description" content="GDC-DNA-Seq-pipeline-galaxy-wrapper - galaxy wrappers GDC-DNA-Seq-pipeline" />
38
39 <link rel="assets" href="https://assets-cdn.github.com/">
40
41 <meta name="pjax-timeout" content="1000">
42
43 <meta name="request-id" content="D1B2:4300:9BB82C:126675F:5B34B7CA" data-pjax-transient>
44
45
46
47
48 <meta name="selected-link" value="repo_source" data-pjax-transient>
49
50 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU">
51 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA">
52 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc">
53 <meta name="google-analytics" content="UA-3769691-2">
54
55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="D1B2:4300:9BB82C:126675F:5B34B7CA" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" />
56 <meta name="analytics-location" content="/&lt;user-name&gt;/&lt;repo-name&gt;" data-pjax-transient="true" />
57
58
59
60
61 <meta class="js-ga-set" name="dimension1" content="Logged Out">
62
63
64
65
66 <meta name="hostname" content="github.com">
67 <meta name="user-login" content="">
68
69 <meta name="expected-hostname" content="github.com">
70 <meta name="js-proxy-site-detection-payload" content="YWJiY2MzOTRjMmI1NWQzNGZhMmEwNmRhOGJkNDZhMjNjODQyYjcwMDE5MDliYmVkMGM3ZjcxZTM4ZGE5NDc5ZXx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJEMUIyOjQzMDA6OUJCODJDOjEyNjY3NUY6NUIzNEI3Q0EiLCJ0aW1lc3RhbXAiOjE1MzAxODE1NzgsImhvc3QiOiJnaXRodWIuY29tIn0=">
71
72 <meta name="enabled-features" content="UNIVERSE_BANNER,FREE_TRIALS,MARKETPLACE_INSIGHTS,MARKETPLACE_SEARCH,MARKETPLACE_INSIGHTS_CONVERSION_PERCENTAGES">
73
74 <meta name="html-safe-nonce" content="42d1ecca95b2c63d38d7750cefb54ab926e76130">
75
76 <meta http-equiv="x-pjax-version" content="f3e765c121ccc4ef016361848b521709">
77
78
79 <link href="https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commits/master.atom" rel="alternate" title="Recent Commits to GDC-DNA-Seq-pipeline-galaxy-wrapper:master" type="application/atom+xml">
80
81 <meta name="description" content="GDC-DNA-Seq-pipeline-galaxy-wrapper - galaxy wrappers GDC-DNA-Seq-pipeline">
82 <meta name="go-import" content="github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper git https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper.git">
83
84 <meta name="octolytics-dimension-user_id" content="39985517" /><meta name="octolytics-dimension-user_login" content="Laniakea-elixir-it" /><meta name="octolytics-dimension-repository_id" content="138863268" /><meta name="octolytics-dimension-repository_nwo" content="Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta name="octolytics-dimension-repository_public" content="true" /><meta name="octolytics-dimension-repository_is_fork" content="true" /><meta name="octolytics-dimension-repository_parent_id" content="128738951" /><meta name="octolytics-dimension-repository_parent_nwo" content="pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta name="octolytics-dimension-repository_network_root_id" content="128738951" /><meta name="octolytics-dimension-repository_network_root_nwo" content="pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" content="false" />
85
86
87 <link rel="canonical" href="https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper" data-pjax-transient>
88
89
90 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
91
92 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
93
94 <link rel="mask-icon" href="https://assets-cdn.github.com/pinned-octocat.svg" color="#000000">
95 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://assets-cdn.github.com/favicon.ico">
96
97 <meta name="theme-color" content="#1e2327">
98
99
100
101 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials">
102
103 </head>
104
105 <body class="logged-out env-production">
106
107
108 <div class="position-relative js-header-wrapper ">
109 <a href="#start-of-content" tabindex="1" class="px-2 py-4 bg-blue text-white show-on-focus js-skip-to-content">Skip to content</a>
110 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div>
111
112
113
114
115
116
117
118 <header class="Header header-logged-out position-relative f4 py-3" role="banner">
119 <div class="container-lg d-flex px-3">
120 <div class="d-flex flex-justify-between flex-items-center">
121 <a class="header-logo-invertocat my-0" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
122 <svg height="32" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
123 </a>
124
125 </div>
126
127 <div class="HeaderMenu HeaderMenu--bright d-flex flex-justify-between flex-auto">
128 <nav class="mt-0">
129 <ul class="d-flex list-style-none">
130 <li class="ml-2">
131 <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:features" data-selected-links="/features /features/project-management /features/code-review /features/project-management /features/integrations /features" href="/features">
132 Features
133 </a> </li>
134 <li class="ml-4">
135 <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:business" data-selected-links="/business /business/security /business/customers /business" href="/business">
136 Business
137 </a> </li>
138
139 <li class="ml-4">
140 <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:explore" data-selected-links="/explore /trending /trending/developers /integrations /integrations/feature/code /integrations/feature/collaborate /integrations/feature/ship showcases showcases_search showcases_landing /explore" href="/explore">
141 Explore
142 </a> </li>
143
144 <li class="ml-4">
145 <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:marketplace" data-selected-links=" /marketplace" href="/marketplace">
146 Marketplace
147 </a> </li>
148 <li class="ml-4">
149 <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:pricing" data-selected-links="/pricing /pricing/developer /pricing/team /pricing/business-hosted /pricing/business-enterprise /pricing" href="/pricing">
150 Pricing
151 </a> </li>
152 </ul>
153 </nav>
154
155 <div class="d-flex">
156 <div class="d-lg-flex flex-items-center mr-3">
157 <div class="header-search scoped-search site-scoped-search js-site-search position-relative js-jump-to"
158 role="search combobox"
159 aria-owns="jump-to-results"
160 aria-label="Search or jump to"
161 aria-haspopup="listbox"
162 aria-expanded="true"
163 >
164 <div class="position-relative">
165 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" data-scope-type="Repository" data-scope-id="138863268" data-scoped-search-url="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/search" data-unscoped-search-url="/search" action="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="&#x2713;" />
166 <label class="form-control header-search-wrapper header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container">
167 <input type="text"
168 class="form-control header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable"
169 data-hotkey="s,/"
170 name="q"
171 value=""
172 placeholder="Search"
173 data-unscoped-placeholder="Search GitHub"
174 data-scoped-placeholder="Search"
175 autocapitalize="off"
176 aria-autocomplete="list"
177 aria-controls="jump-to-results"
178 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=6lUc/uptFaM8GikLb0P8dA+DqI98yzbKvbQirGsULtmxTnXNokRJg/nP2l83HaUxDs+U1iqFhxx2o3Kmt4L3qw=="
179 spellcheck="false"
180 autocomplete="off"
181 >
182 <input type="hidden" class="js-site-search-type-field" name="type" >
183 <img src="https://assets-cdn.github.com/images/search-shortcut-hint.svg" alt="" class="mr-2 header-search-key-slash">
184
185 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
186 <ul class="d-none js-jump-to-suggestions-template-container">
187 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item">
188 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center p-2 jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open" href="">
189 <div class="jump-to-octicon js-jump-to-octicon mr-2 text-center d-none"></div>
190 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar" alt="" aria-label="Team" src="" width="28" height="28">
191
192 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden no-wrap css-truncate css-truncate-target">
193 </div>
194
195 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
196 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
197 In this repository
198 </span>
199 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
200 All GitHub
201 </span>
202 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
203 </div>
204
205 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
206 Jump to
207 <span class="d-inline-block ml-1 v-align-middle">↵</span>
208 </div>
209 </a>
210 </li>
211 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-repo-octicon-template" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
212 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-project-octicon-template" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
213 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-search-octicon-template" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
214 </ul>
215 <ul class="d-none js-jump-to-no-results-template-container">
216 <li class="d-flex flex-justify-center flex-items-center p-3 f5 d-none">
217 <span class="text-gray">No suggested jump to results</span>
218 </li>
219 </ul>
220
221 <ul id="jump-to-results" class="js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container" >
222 <li class="d-flex flex-justify-center flex-items-center p-0 f5">
223 <img src="https://assets-cdn.github.com/images/spinners/octocat-spinner-128.gif" alt="Octocat Spinner Icon" class="m-2" width="28">
224 </li>
225 </ul>
226 </div>
227 </label>
228 </form> </div>
229 </div>
230
231 </div>
232
233 <span class="d-inline-block">
234 <div class="HeaderNavlink px-0 py-2 m-0">
235 <a class="text-bold text-white no-underline" href="/login?return_to=%2FLaniakea-elixir-it%2FGDC-DNA-Seq-pipeline-galaxy-wrapper" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a>
236 <span class="text-gray">or</span>
237 <a class="text-bold text-white no-underline" href="/join?source=header-repo" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a>
238 </div>
239 </span>
240 </div>
241 </div>
242 </div>
243 </header>
244
245 </div>
246
247 <div id="start-of-content" class="show-on-focus"></div>
248
249 <div id="js-flash-container">
250 </div>
251
252
253
254 <div role="main" class="application-main ">
255 <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class="">
256 <div id="js-repo-pjax-container" data-pjax-container >
257
258
259
260
261
262
263
264
265 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav ">
266 <div class="repohead-details-container clearfix container">
267
268 <ul class="pagehead-actions">
269 <li>
270 <a href="/login?return_to=%2FLaniakea-elixir-it%2FGDC-DNA-Seq-pipeline-galaxy-wrapper"
271 class="btn btn-sm btn-with-count tooltipped tooltipped-n"
272 aria-label="You must be signed in to watch a repository" rel="nofollow">
273 <svg class="octicon octicon-eye" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg>
274 Watch
275 </a>
276 <a class="social-count" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/watchers"
277 aria-label="1 user is watching this repository">
278 1
279 </a>
280
281 </li>
282
283 <li>
284 <a href="/login?return_to=%2FLaniakea-elixir-it%2FGDC-DNA-Seq-pipeline-galaxy-wrapper"
285 class="btn btn-sm btn-with-count tooltipped tooltipped-n"
286 aria-label="You must be signed in to star a repository" rel="nofollow">
287 <svg class="octicon octicon-star" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74L14 6z"/></svg>
288 Star
289 </a>
290
291 <a class="social-count js-social-count" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/stargazers"
292 aria-label="0 users starred this repository">
293 0
294 </a>
295
296 </li>
297
298 <li>
299 <a href="/login?return_to=%2FLaniakea-elixir-it%2FGDC-DNA-Seq-pipeline-galaxy-wrapper"
300 class="btn btn-sm btn-with-count tooltipped tooltipped-n"
301 aria-label="You must be signed in to fork a repository" rel="nofollow">
302 <svg class="octicon octicon-repo-forked" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
303 Fork
304 </a>
305
306 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/network" class="social-count"
307 aria-label="1 user forked this repository">
308 1
309 </a>
310 </li>
311 </ul>
312
313 <h1 class="public ">
314 <svg class="octicon octicon-repo-forked" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
315 <span class="author" itemprop="author"><a class="url fn" rel="author" href="/Laniakea-elixir-it">Laniakea-elixir-it</a></span><!--
316 --><span class="path-divider">/</span><!--
317 --><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper">GDC-DNA-Seq-pipeline-galaxy-wrapper</a></strong>
318
319 <span class="fork-flag">
320 <span class="text">forked from <a href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper">pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper</a></span>
321 </span>
322 </h1>
323
324 </div>
325
326 <nav class="reponav js-repo-nav js-sidenav-container-pjax container"
327 itemscope
328 itemtype="http://schema.org/BreadcrumbList"
329 role="navigation"
330 data-pjax="#js-repo-pjax-container">
331
332 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
333 <a class="js-selected-navigation-item selected reponav-item" itemprop="url" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper">
334 <svg class="octicon octicon-code" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg>
335 <span itemprop="name">Code</span>
336 <meta itemprop="position" content="1">
337 </a> </span>
338
339
340 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
341 <a data-hotkey="g p" itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulls" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulls">
342 <svg class="octicon octicon-git-pull-request" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
343 <span itemprop="name">Pull requests</span>
344 <span class="Counter">0</span>
345 <meta itemprop="position" content="3">
346 </a> </span>
347
348 <a data-hotkey="g b" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/projects" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/projects">
349 <svg class="octicon octicon-project" viewBox="0 0 15 16" version="1.1" width="15" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
350 Projects
351 <span class="Counter" >0</span>
352 </a>
353
354
355 <a class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors dependency_graph pulse /Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulse" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulse">
356 <svg class="octicon octicon-graph" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg>
357 Insights
358 </a>
359
360 </nav>
361
362
363 </div>
364
365 <div class="container new-discussion-timeline experiment-repo-nav ">
366 <div class="repository-content ">
367
368
369 <div class="signup-prompt-bg rounded-1">
370 <div class="signup-prompt p-4 text-center mb-4 rounded-1">
371 <div class="position-relative">
372 <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/site/dismiss_signup_prompt" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="&#x2713;" /><input type="hidden" name="authenticity_token" value="QJkc+KT06NGtYE7EK/x5TYBkwvIe59C89h+cXCnScw3ol8G6EJfMNsSZFIIvEKna5z21QcChzqQQkqkuGf6E4w==" />
373 <button type="submit" class="position-absolute top-0 right-0 btn-link link-gray" data-ga-click="(Logged out) Sign up prompt, clicked Dismiss, text:dismiss">
374 Dismiss
375 </button>
376 </form> <h3 class="pt-2">Join GitHub today</h3>
377 <p class="col-6 mx-auto">GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.</p>
378 <a class="btn btn-primary" href="/join?source=prompt-code" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up">Sign up</a>
379 </div>
380 </div>
381 </div>
382
383
384 <div class="js-repo-meta-container">
385 <div class="repository-meta mb-0 mb-3 js-repo-meta-edit js-details-container ">
386 <div class="repository-meta-content col-11 mb-1">
387 <span class="col-11 text-gray-dark mr-2" itemprop="about">
388 galaxy wrappers GDC-DNA-Seq-pipeline
389 </span>
390 </div>
391
392 </div>
393
394 </div>
395
396
397
398 <div class="overall-summary overall-summary-bottomless">
399 <div class="stats-switcher-viewport js-stats-switcher-viewport">
400 <div class="stats-switcher-wrapper">
401 <ul class="numbers-summary">
402 <li class="commits">
403 <a data-pjax href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commits/master">
404 <svg class="octicon octicon-history" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 13H6V6h5v2H8v5zM7 1C4.81 1 2.87 2.02 1.59 3.59L0 2v4h4L2.5 4.5C3.55 3.17 5.17 2.3 7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-.34.03-.67.09-1H.08C.03 7.33 0 7.66 0 8c0 3.86 3.14 7 7 7s7-3.14 7-7-3.14-7-7-7z"/></svg>
405 <span class="num text-emphasized">
406 85
407 </span>
408 commits
409 </a>
410 </li>
411 <li>
412 <a data-pjax href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/branches">
413 <svg class="octicon octicon-git-branch" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M10 5c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v.3c-.02.52-.23.98-.63 1.38-.4.4-.86.61-1.38.63-.83.02-1.48.16-2 .45V4.72a1.993 1.993 0 0 0-1-3.72C.88 1 0 1.89 0 3a2 2 0 0 0 1 1.72v6.56c-.59.35-1 .99-1 1.72 0 1.11.89 2 2 2 1.11 0 2-.89 2-2 0-.53-.2-1-.53-1.36.09-.06.48-.41.59-.47.25-.11.56-.17.94-.17 1.05-.05 1.95-.45 2.75-1.25S8.95 7.77 9 6.73h-.02C9.59 6.37 10 5.73 10 5zM2 1.8c.66 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2C1.35 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2zm0 12.41c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm6-8c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
414 <span class="num text-emphasized">
415 3
416 </span>
417 branches
418 </a>
419 </li>
420
421 <li>
422 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/releases">
423 <svg class="octicon octicon-tag" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.685 1.72a2.49 2.49 0 0 0-1.76-.726H3.48A2.5 2.5 0 0 0 .994 3.48v2.456c0 .656.269 1.292.726 1.76l6.024 6.024a.99.99 0 0 0 1.402 0l4.563-4.563a.99.99 0 0 0 0-1.402L7.685 1.72zM2.366 7.048A1.54 1.54 0 0 1 1.9 5.925V3.48c0-.874.716-1.58 1.58-1.58h2.456c.418 0 .825.159 1.123.467l6.104 6.094-4.702 4.702-6.094-6.114zm.626-4.066h1.989v1.989H2.982V2.982h.01z"/></svg>
424 <span class="num text-emphasized">
425 0
426 </span>
427 releases
428 </a>
429 </li>
430
431 <li>
432 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/graphs/contributors">
433 <svg class="octicon octicon-organization" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 12.999c0 .439-.45 1-1 1H7.995c-.539 0-.994-.447-.995-.999H1c-.54 0-1-.561-1-1 0-2.634 3-4 3-4s.229-.409 0-1c-.841-.621-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.442.58 2.5 3c.058 2.41-.159 2.379-1 3-.229.59 0 1 0 1s1.549.711 2.42 2.088C9.196 9.369 10 8.999 10 8.999s.229-.409 0-1c-.841-.62-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.437.581 2.495 3c.059 2.41-.158 2.38-1 3-.229.59 0 1 0 1s3.005 1.366 3.005 4z"/></svg>
434 <span class="num text-emphasized">
435 2
436 </span>
437 contributors
438 </a>
439
440 </li>
441 <li>
442 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/LICENSE">
443 <svg class="octicon octicon-law" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7 4c-.83 0-1.5-.67-1.5-1.5S6.17 1 7 1s1.5.67 1.5 1.5S7.83 4 7 4zm7 6c0 1.11-.89 2-2 2h-1c-1.11 0-2-.89-2-2l2-4h-1c-.55 0-1-.45-1-1H8v8c.42 0 1 .45 1 1h1c.42 0 1 .45 1 1H3c0-.55.58-1 1-1h1c0-.55.58-1 1-1h.03L6 5H5c0 .55-.45 1-1 1H3l2 4c0 1.11-.89 2-2 2H2c-1.11 0-2-.89-2-2l2-4H1V5h3c0-.55.45-1 1-1h4c.55 0 1 .45 1 1h3v1h-1l2 4zM2.5 7L1 10h3L2.5 7zM13 10l-1.5-3-1.5 3h3z"/></svg>
444 MIT
445 </a>
446 </li>
447 </ul>
448
449 <div class="repository-lang-stats">
450 <ol class="repository-lang-stats-numbers">
451 <li>
452 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/search?l=perl" data-ga-click="Repository, language stats search click, location:repo overview">
453 <span class="color-block language-color" style="background-color:#0298c3;"></span>
454 <span class="lang">Perl</span>
455 <span class="percent">100.0%</span>
456 </a>
457 </li>
458 </ol>
459 </div>
460 </div>
461 </div>
462 </div>
463
464 <div class="repository-lang-stats-graph js-toggle-lang-stats" title="Click for language details" data-ga-click="Repository, language bar stats toggle, location:repo overview">
465 <span class="language-color" aria-label="Perl 100.0%" style="width:100.0%; background-color:#0298c3;" itemprop="keywords">Perl</span>
466 </div>
467
468
469
470
471 <div class="file-navigation in-mid-page d-flex flex-items-start">
472
473 <div class="select-menu branch-select-menu js-menu-container js-select-menu float-left">
474 <button class=" btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w"
475
476 type="button" aria-label="Switch branches or tags" aria-expanded="false" aria-haspopup="true">
477 <i>Branch:</i>
478 <span class="js-select-button css-truncate-target">master</span>
479 </button>
480
481 <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax>
482
483 <div class="select-menu-modal">
484 <div class="select-menu-header">
485 <svg class="octicon octicon-x js-menu-close" role="img" aria-label="Close" viewBox="0 0 12 16" version="1.1" width="12" height="16"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
486 <span class="select-menu-title">Switch branches/tags</span>
487 </div>
488
489 <div class="select-menu-filters">
490 <div class="select-menu-text-filter">
491 <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="form-control js-filterable-field js-navigation-enable" placeholder="Filter branches/tags">
492 </div>
493 <div class="select-menu-tabs">
494 <ul>
495 <li class="select-menu-tab">
496 <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a>
497 </li>
498 <li class="select-menu-tab">
499 <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab" role="tab">Tags</a>
500 </li>
501 </ul>
502 </div>
503 </div>
504
505 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu">
506
507 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
508
509
510 <a class="select-menu-item js-navigation-item js-navigation-open "
511 href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/dev"
512 data-name="dev"
513 data-skip-pjax="true"
514 rel="nofollow">
515 <svg class="octicon octicon-check select-menu-item-icon" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5L12 5z"/></svg>
516 <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text">
517 dev
518 </span>
519 </a>
520 <a class="select-menu-item js-navigation-item js-navigation-open selected"
521 href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master"
522 data-name="master"
523 data-skip-pjax="true"
524 rel="nofollow">
525 <svg class="octicon octicon-check select-menu-item-icon" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5L12 5z"/></svg>
526 <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text">
527 master
528 </span>
529 </a>
530 <a class="select-menu-item js-navigation-item js-navigation-open "
531 href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/test"
532 data-name="test"
533 data-skip-pjax="true"
534 rel="nofollow">
535 <svg class="octicon octicon-check select-menu-item-icon" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5L12 5z"/></svg>
536 <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text">
537 test
538 </span>
539 </a>
540 </div>
541
542 <div class="select-menu-no-results">Nothing to show</div>
543 </div>
544
545 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags">
546 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
547
548
549 </div>
550
551 <div class="select-menu-no-results">Nothing to show</div>
552 </div>
553
554 </div>
555 </div>
556 </div>
557
558
559 <button type="button" class="btn btn-sm disabled tooltipped tooltipped-n new-pull-request-btn" aria-label="You must be signed in to create a pull request">
560 New pull request
561 </button>
562
563 <div class="breadcrumb flex-auto">
564
565 </div>
566
567 <div class="BtnGroup">
568
569 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/find/master"
570 class="btn btn-sm empty-icon float-right BtnGroup-item"
571 data-pjax
572 data-hotkey="t"
573 data-ga-click="Repository, find file, location:repo overview">
574 Find file
575 </a>
576 </div>
577
578
579 <details class="get-repo-select-menu js-get-repo-select-menu position-relative details-overlay details-reset">
580 <summary class="btn btn-sm btn-primary">
581 Clone or download
582 <span class="dropdown-caret"></span>
583 </summary>
584 <div class="position-relative">
585 <div class="get-repo-modal dropdown-menu dropdown-menu-sw pb-0 js-toggler-container js-get-repo-modal">
586
587 <div class="get-repo-modal-options">
588 <div class="clone-options https-clone-options">
589
590 <h4 class="mb-1">
591 Clone with HTTPS
592 <a class="muted-link" href="https://help.github.com/articles/which-remote-url-should-i-use" target="_blank" title="Which remote URL should I use?">
593 <svg class="octicon octicon-question" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 10h2v2H6v-2zm4-3.5C10 8.64 8 9 8 9H6c0-.55.45-1 1-1h.5c.28 0 .5-.22.5-.5v-1c0-.28-.22-.5-.5-.5h-1c-.28 0-.5.22-.5.5V7H4c0-1.5 1.5-3 3-3s3 1 3 2.5zM7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7z"/></svg>
594 </a>
595 </h4>
596 <p class="mb-2 get-repo-decription-text">
597 Use Git or checkout with SVN using the web URL.
598 </p>
599
600 <div class="input-group">
601 <input type="text" class="form-control input-monospace input-sm js-url-field" value="https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper.git" aria-label="Clone this repository at https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper.git" readonly>
602 <div class="input-group-button">
603 <clipboard-copy value="https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper.git" aria-label="Copy to clipboard" class="btn btn-sm">
604 <svg class="octicon octicon-clippy" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M2 13h4v1H2v-1zm5-6H2v1h5V7zm2 3V8l-3 3 3 3v-2h5v-2H9zM4.5 9H2v1h2.5V9zM2 12h2.5v-1H2v1zm9 1h1v2c-.02.28-.11.52-.3.7-.19.18-.42.28-.7.3H1c-.55 0-1-.45-1-1V4c0-.55.45-1 1-1h3c0-1.11.89-2 2-2 1.11 0 2 .89 2 2h3c.55 0 1 .45 1 1v5h-1V6H1v9h10v-2zM2 5h8c0-.55-.45-1-1-1H8c-.55 0-1-.45-1-1s-.45-1-1-1-1 .45-1 1-.45 1-1 1H3c-.55 0-1 .45-1 1z"/></svg>
605 </clipboard-copy>
606 </div>
607 </div>
608
609 </div>
610
611 <div class="mt-2">
612
613 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/archive/master.zip"
614 class="btn btn-outline get-repo-btn
615 "
616 rel="nofollow"
617 data-ga-click="Repository, download zip, location:repo overview">
618 Download ZIP
619 </a>
620
621 </div>
622 </div>
623
624 <div class="js-modal-download-mac py-2 px-3 d-none">
625 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
626 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
627 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
628 </div>
629
630 <div class="js-modal-download-windows py-2 px-3 d-none">
631 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
632 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
633 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
634 </div>
635
636 <div class="js-modal-download-xcode py-2 px-3 d-none">
637 <h4 class="lh-condensed mb-3">Launching Xcode<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
638 <p class="text-gray">If nothing happens, <a href="https://developer.apple.com/xcode/">download Xcode</a> and try again.</p>
639 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
640 </div>
641
642 <div class="js-modal-download-visual-studio py-2 px-3 d-none">
643 <h4 class="lh-condensed mb-3">Launching Visual Studio<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
644 <p class="text-gray">If nothing happens, <a href="https://visualstudio.github.com/">download the GitHub extension for Visual Studio</a> and try again.</p>
645 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
646 </div>
647
648 </div>
649 </div>
650 </details>
651
652 </div>
653
654
655
656 <div class="branch-infobar">
657 <span class="float-right">
658 <a class="muted-link" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/pull/new/master">
659 <svg class="octicon octicon-git-pull-request" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
660 Pull request
661 </a>
662 <a class="muted-link" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/compare">
663 <svg class="octicon octicon-diff" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 7h2v1H6v2H5V8H3V7h2V5h1v2zm-3 6h5v-1H3v1zM7.5 2L11 5.5V15c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V3c0-.55.45-1 1-1h6.5zM10 6L7 3H1v12h9V6zM8.5 0H3v1h5l4 4v8h1V4.5L8.5 0z"/></svg>
664 Compare
665 </a>
666 </span>
667
668 This branch is 9 commits ahead of pmandreoli:master.
669 </div>
670
671
672 <div class="commit-tease js-details-container Details d-flex">
673
674 <div class="AvatarStack flex-self-start ">
675 <div class="AvatarStack-body" aria-label="pmandreoli">
676
677 <a class="avatar" data-skip-pjax="true" data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli">
678 <img height="20" width="20" alt="@pmandreoli" src="https://avatars3.githubusercontent.com/u/33326058?s=60&amp;v=4" />
679 </a> </div>
680 </div>
681
682 <div class="flex-auto f6 no-wrap mr-3">
683
684 <a href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commits?author=pmandreoli"
685 class="commit-author tooltipped tooltipped-s user-mention"
686 aria-label="View all commits by pmandreoli">pmandreoli</a>
687
688
689
690
691
692 <a data-pjax="true" title="order_change" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/0816edd870fef962e6ab76a7d831917a6ef6a6c3">order_change</a>
693
694 </div>
695 <div class="no-wrap">
696 Latest commit
697 <a class="commit-tease-sha" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/0816edd870fef962e6ab76a7d831917a6ef6a6c3" data-pjax>
698 0816edd
699 </a>
700 <span itemprop="dateModified"><relative-time datetime="2018-06-28T09:30:36Z">Jun 28, 2018</relative-time></span>
701 </div>
702 </div>
703
704
705
706 <div class="file-wrap">
707
708 <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/0816edd870fef962e6ab76a7d831917a6ef6a6c3">Permalink</a>
709
710 <table class="files js-navigation-container js-active-navigation-container" data-pjax>
711
712
713 <tbody>
714 <tr class="warning include-fragment-error">
715 <td class="icon"><svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg></td>
716 <td class="content" colspan="3">Failed to load latest commit information.</td>
717 </tr>
718
719 <tr class="js-navigation-item">
720 <td class="icon">
721 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
722 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
723 </td>
724 <td class="content">
725 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="MuSE-wrappers" id="6eeb64d3373c86de0d266d51ca7aad6d-5ad7ff1d5254207913649df43ac24dc94ce9beeb" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/MuSE-wrappers">MuSE-wrappers</a></span>
726 </td>
727 <td class="message">
728 <span class="css-truncate css-truncate-target">
729 <a data-pjax="true" title="renamed" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/db217a791b5adeaaa396e6410f590f1dd083f56b">renamed</a>
730 </span>
731 </td>
732 <td class="age">
733 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-27T09:27:20Z">Jun 27, 2018</time-ago></span>
734 </td>
735 </tr>
736 <tr class="js-navigation-item">
737 <td class="icon">
738 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
739 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
740 </td>
741 <td class="content">
742 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="Mutect2-wrapper" id="7298d96c43b1f2394bd6e17cfdc622b3-1a6e9b10f4bd715c4d31f566f5c8c71f23c20915" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/Mutect2-wrapper">Mutect2-wrapper</a></span>
743 </td>
744 <td class="message">
745 <span class="css-truncate css-truncate-target">
746 <a data-pjax="true" title="order_change" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/0816edd870fef962e6ab76a7d831917a6ef6a6c3">order_change</a>
747 </span>
748 </td>
749 <td class="age">
750 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-28T09:30:36Z">Jun 28, 2018</time-ago></span>
751 </td>
752 </tr>
753 <tr class="js-navigation-item">
754 <td class="icon">
755 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
756 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
757 </td>
758 <td class="content">
759 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="fpfilter-wrapper" id="b8e9ac11418f2ca943696e2ae7ade2c1-03fccac761b2e73a7c7aa57e407595df6d73c94f" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/fpfilter-wrapper">fpfilter-wrapper</a></span>
760 </td>
761 <td class="message">
762 <span class="css-truncate css-truncate-target">
763 <a data-pjax="true" title="test-data" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/cb43d2cf8d3a96e3538290dbbcabd35eb0241ae2">test-data</a>
764 </span>
765 </td>
766 <td class="age">
767 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-05-11T09:58:45Z">May 11, 2018</time-ago></span>
768 </td>
769 </tr>
770 <tr class="js-navigation-item">
771 <td class="icon">
772 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
773 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
774 </td>
775 <td class="content">
776 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="somatic-sniper-wrapper" id="fb1b18b4869b8add123840bcbf1c8ec4-47b039289242e13ff648b40e41af303faaca601f" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/somatic-sniper-wrapper">somatic-sniper-wrapper</a></span>
777 </td>
778 <td class="message">
779 <span class="css-truncate css-truncate-target">
780 <a data-pjax="true" title="test_part" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/8b532e1bd87b7cf17059e325a60ed6cef0ea05df">test_part</a>
781 </span>
782 </td>
783 <td class="age">
784 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-22T13:15:39Z">Jun 22, 2018</time-ago></span>
785 </td>
786 </tr>
787 <tr class="js-navigation-item">
788 <td class="icon">
789 <svg class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
790 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
791 </td>
792 <td class="content">
793 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="vep86_vcf2maf-wrapper" id="e38ee16d2b256818c33d0541312f040c-78cb195337d66a39abb4661691074ba92f4425b9" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/vep86_vcf2maf-wrapper">vep86_vcf2maf-wrapper</a></span>
794 </td>
795 <td class="message">
796 <span class="css-truncate css-truncate-target">
797 <a data-pjax="true" title="renamed" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/db217a791b5adeaaa396e6410f590f1dd083f56b">renamed</a>
798 </span>
799 </td>
800 <td class="age">
801 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-27T09:27:20Z">Jun 27, 2018</time-ago></span>
802 </td>
803 </tr>
804 <tr class="js-navigation-item">
805 <td class="icon">
806 <svg class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
807 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
808 </td>
809 <td class="content">
810 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="LICENSE" id="9879d6db96fd29134fc802214163b95a-4eb8dbddf70d795e05ea7b0e726ad57a2518ac6d" itemprop="license" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/LICENSE">LICENSE</a></span>
811 </td>
812 <td class="message">
813 <span class="css-truncate css-truncate-target">
814 <a data-pjax="true" title="Initial commit" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/7113c7c00c0852eae67102e479346822ef3c2c81">Initial commit</a>
815 </span>
816 </td>
817 <td class="age">
818 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-04-09T08:25:03Z">Apr 9, 2018</time-ago></span>
819 </td>
820 </tr>
821 <tr class="js-navigation-item">
822 <td class="icon">
823 <svg class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
824 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
825 </td>
826 <td class="content">
827 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="README.md" id="04c6e90faac2675aa89e2176d2eec7d8-d5bc11a7b913ef494c676b275fae35a4760c6956" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/README.md">README.md</a></span>
828 </td>
829 <td class="message">
830 <span class="css-truncate css-truncate-target">
831 <a data-pjax="true" title="update" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/6ec4b8217c8c8ae7e98e3038190524b82617a3e6">update</a>
832 </span>
833 </td>
834 <td class="age">
835 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-06-27T13:37:21Z">Jun 27, 2018</time-ago></span>
836 </td>
837 </tr>
838 <tr class="js-navigation-item">
839 <td class="icon">
840 <svg class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
841 <img width="16" height="16" class="spinner" alt="" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" />
842 </td>
843 <td class="content">
844 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="shed_tool_add.xml" id="35140ba3b6329aea1a67251631945339-0f848762d0c898cba30bbfad90c44f9ba4ea4243" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/shed_tool_add.xml">shed_tool_add.xml</a></span>
845 </td>
846 <td class="message">
847 <span class="css-truncate css-truncate-target">
848 <a data-pjax="true" title="config_file" class="message" href="/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/f2c7a2ea607b05d784ff44f699af85e9b06f2742">config_file</a>
849 </span>
850 </td>
851 <td class="age">
852 <span class="css-truncate css-truncate-target"><time-ago datetime="2018-05-10T14:21:46Z">May 10, 2018</time-ago></span>
853 </td>
854 </tr>
855 </tbody>
856 </table>
857
858 </div>
859
860
861
862 <div id="readme" class="readme boxed-group clearfix announce instapaper_body md">
863 <h3>
864 <svg class="octicon octicon-book" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M3 5h4v1H3V5zm0 3h4V7H3v1zm0 2h4V9H3v1zm11-5h-4v1h4V5zm0 2h-4v1h4V7zm0 2h-4v1h4V9zm2-6v9c0 .55-.45 1-1 1H9.5l-1 1-1-1H2c-.55 0-1-.45-1-1V3c0-.55.45-1 1-1h5.5l1 1 1-1H15c.55 0 1 .45 1 1zm-8 .5L7.5 3H2v9h6V3.5zm7-.5H9.5l-.5.5V12h6V3z"/></svg>
865 README.md
866 </h3>
867
868 <article class="markdown-body entry-content" itemprop="text"><h1><a id="user-content-gdc-dna-seq-pipeline-galaxy-wrapper" class="anchor" aria-hidden="true" href="#gdc-dna-seq-pipeline-galaxy-wrapper"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>GDC-DNA-Seq-pipeline-galaxy-wrapper</h1>
869 <p>The GDC DNA-Seq analysis pipeline identifies somatic variants within whole exome sequencing (WXS) and whole genome sequencing (WGS) data. Somatic variants are identified by comparing allele frequencies in normal and tumor sample alignments, annotating each mutation, and aggregating mutations from multiple cases into one project file.</p>
870 <p>The first pipeline starts with a reference alignment step followed by co-cleaning to increase the alignment quality. Four different variant calling pipelines are then implemented separately to identify somatic mutations. Somatic-caller-identified variants are then annotated. An aggregation pipeline incorporates variants from all cases in one project into a MAF file for each pipeline.</p>
871 <p>DNA-Seq analysis is implemented across six main procedures:</p>
872 <ul>
873 <li>Genome Alignment</li>
874 <li>Alignment Co-Cleaning</li>
875 <li>Somatic Variant Calling</li>
876 <li>Variant Annotation</li>
877 <li>Mutation Aggregation</li>
878 </ul>
879 <p><strong>Genome Alignment</strong></p>
880 <p>Read groups are aligned to the reference genome BWA-MEM if mean read length is greater than or equal to 70 bp. Otherwise BWA-aln is used.
881 Each read group is aligned to the reference genome separately and all read group alignments that belong to a single aliquot are merged using SortSam and MergeSamFiles (Picard Tools).</p>
882 <p><strong>Co-cleaning Workflow</strong></p>
883 <p>Co-cleaning is performed as a separate pipeline as it uses multiple BAM files (i.e. the tumor BAM and normal tissue BAM) associated with the same patient. Both steps of this process are implemented using GATK</p>
884 <pre><code>* Local realignment of insertions and deletions is performed using IndelRealigner
885 * A base quality score recalibration (BQSR) step is then performed using BaseRecalibrator.
886 * A filter reads step is preformed by Printreads
887 </code></pre>
888 <p><strong>Somatic Variant Calling</strong></p>
889 <p>Aligned and co-cleaned BAM files are processed through the Somatic Mutation Calling Workflow as tumor-normal pairs.
890 Variant calling is performed using four separate pipelines:</p>
891 <pre><code>* MuSE
892 * MuTect2
893 * VarScan2
894 * SomaticSniper
895 </code></pre>
896 <p><strong>Variant Call Annotation Workflow</strong></p>
897 <p>Raw VCF files are then annotated in the Somatic Annotation Workflow with the Variant Effect Predictor v84
898 In addition to annotation False Positive Filter is used to label low quality variants in VarScan and SomaticSniper outputs.</p>
899 <p><strong>Somatic Agregation Workflow</strong></p>
900 <p>multiple vcf file can merged and using vcf2maf a MAF file from multiple vcf can be created.</p>
901 <p>#More informations at
902 <a href="https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#file-access-and-availability" rel="nofollow">https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#file-access-and-availability</a></p>
903 <p><em>All the tools and option used in the command line pipeline can be used throught galaxy wrappers</em></p>
904 </article>
905 </div>
906
907
908 </div>
909 <div class="modal-backdrop js-touch-events"></div>
910 </div>
911
912 </div>
913 </div>
914
915 </div>
916
917
918 <div class="footer container-lg px-3" role="contentinfo">
919 <div class="position-relative d-flex flex-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light ">
920 <ul class="list-style-none d-flex flex-wrap ">
921 <li class="mr-3">&copy; 2018 <span title="0.30493s from unicorn-5bd596f84d-7rsk8">GitHub</span>, Inc.</li>
922 <li class="mr-3"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li>
923 <li class="mr-3"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li>
924 <li class="mr-3"><a href="https://help.github.com/articles/github-security/" data-ga-click="Footer, go to security, text:security">Security</a></li>
925 <li class="mr-3"><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
926 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
927 </ul>
928
929 <a aria-label="Homepage" title="GitHub" class="footer-octicon" href="https://github.com">
930 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
931 </a>
932 <ul class="list-style-none d-flex flex-wrap ">
933 <li class="mr-3"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li>
934 <li class="mr-3"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
935 <li class="mr-3"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
936 <li class="mr-3"><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li>
937 <li class="mr-3"><a href="https://blog.github.com" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
938 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
939
940 </ul>
941 </div>
942 <div class="d-flex flex-justify-center pb-6">
943 <span class="f6 text-gray-light"></span>
944 </div>
945 </div>
946
947
948
949 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
950 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
951 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
952 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
953 </button>
954 You can’t perform that action at this time.
955 </div>
956
957
958 <script crossorigin="anonymous" integrity="sha512-wIuAKDhvxe9wCaNR1tzCk3rtl+wXEWC28rmRpzmx0h98VEeWC6Y3xCWV1xAW6NP6eQQX+x8ZGhW6Sdut+mLRuw==" type="application/javascript" src="https://assets-cdn.github.com/assets/compat-a48960bafc17c30572990bbab3664e9c.js"></script>
959 <script crossorigin="anonymous" integrity="sha512-rQ5rqxNcZevFDDt0YpFyUsMdf6ORyN1evQjIGwQGbiIaLrROmN77NgRxz+EOtW1VEo75v97gppFprSCKLq0s9w==" type="application/javascript" src="https://assets-cdn.github.com/assets/frameworks-6ad64ae8a533d7550b0f4b5b12d08ee7.js"></script>
960
961 <script crossorigin="anonymous" async="async" integrity="sha512-MluPTi4ElJIVCIU3rFJ7lVukR7SJi6Bhws96FO91NpNHbE7Mnf5ymDBf6e+xJKQr4xzw/5XrjvrNmdnVGNSagg==" type="application/javascript" src="https://assets-cdn.github.com/assets/github-9e1fb62f0965afe7d5d91ca5b5c1e71d.js"></script>
962
963
964
965 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner d-none">
966 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
967 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
968 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
969 </div>
970 <div class="facebox" id="facebox" style="display:none;">
971 <div class="facebox-popup">
972 <div class="facebox-content" role="dialog" aria-labelledby="facebox-header" aria-describedby="facebox-description">
973 </div>
974 <button type="button" class="facebox-close js-facebox-close" aria-label="Close modal">
975 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
976 </button>
977 </div>
978 </div>
979
980 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
981 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
982 </div>
983 </div>
984
985 <div id="hovercard-aria-description" class="sr-only">
986 Press h to open a hovercard with more details.
987 </div>
988
989
990 </body>
991 </html>
992