-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Deployed 0140a9f to latest with MkDocs 1.6.0 and mike 2.0.0
- Loading branch information
1 parent
bc64820
commit ac2f8b5
Showing
21 changed files
with
169 additions
and
106 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -12,7 +12,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="/viralgenie/latest/images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -993,7 +993,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": "/viralgenie/latest", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "/viralgenie/latest/assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="/viralgenie/latest/assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="/viralgenie/latest/assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,7 +18,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="../images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -1477,7 +1477,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": "..", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="../assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="../assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -16,7 +16,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="../images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -1490,7 +1490,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": "..", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="../assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="../assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
10 changes: 5 additions & 5 deletions
10
...assets/javascripts/bundle.3220b9d7.min.js → ...assets/javascripts/bundle.dd8806f2.min.js
Large diffs are not rendered by default.
Oops, something went wrong.
6 changes: 3 additions & 3 deletions
6
...ts/javascripts/bundle.3220b9d7.min.js.map → ...ts/javascripts/bundle.dd8806f2.min.js.map
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,7 +18,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="../../images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -1198,7 +1198,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": "../..", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "../../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="../../assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="../../assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,7 +18,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="../../images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -1511,7 +1511,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": "../..", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "../../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="../../assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="../../assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,7 +18,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -914,6 +914,7 @@ <h2 id="pipeline-summary">Pipeline summary</h2> | |
| <li>Metagenomic diveristy mapping<ul> | ||
| <li>Performs taxonomic classification and/or profiling using one or more of:<ul> | ||
| <li><a href="https://ccb.jhu.edu/software/kraken2/"><code>Kraken2</code></a></li> | ||
| <li><a href="https://ccb.jhu.edu/software/bracken/"><code>Bracken</code></a>[optional]</li> | ||
| <li><a href="https://kaiju.binf.ku.dk/"><code>Kaiju</code></a></li> | ||
| </ul> | ||
| </li> | ||
|
|
@@ -927,8 +928,8 @@ <h2 id="pipeline-summary">Pipeline summary</h2> | |
| </ul> | ||
| </li> | ||
| <li>[Optional] Precluster contigs based on taxonomy<ul> | ||
| <li>Identify taxonomy <a href="https://ccb.jhu.edu/software/kraken2/"><code>Kraken2</code></a> and <a href="https://kaiju.binf.ku.dk/"><code>Kaiju</code></a></li> | ||
| <li>Resolve potential incosistencies in taxonomy <a href="https://kaiju.binf.ku.dk/"><code>Kaiju-mergeOutputs</code></a></li> | ||
| <li>Identify taxonomy <a href="https://ccb.jhu.edu/software/kraken2/"><code>Kraken2</code></a> and\or <a href="https://kaiju.binf.ku.dk/"><code>Kaiju</code></a></li> | ||
| <li>Resolve potential inconsistencies in taxonomy & taxon filtering | simplification <code>bin/extract_precluster.py</code></li> | ||
| </ul> | ||
| </li> | ||
| <li>Cluster contigs (or every taxonomic bin) of samples, options are:<ul> | ||
|
|
@@ -941,7 +942,7 @@ <h2 id="pipeline-summary">Pipeline summary</h2> | |
| </ul> | ||
| </li> | ||
| <li>Scaffolding of contigs to centroid (<a href="https://github.com/lh3/minimap2"><code>Minimap2</code></a>, <a href="https://andersen-lab.github.io/ivar/html/manualpage.html"><code>iVar-consensus</code></a>)</li> | ||
| <li>[Optional] Annotate 0-depth regions with external reference <code>custom-script</code>.</li> | ||
| <li>[Optional] Annotate 0-depth regions with external reference <code>bin/lowcov_to_reference.py</code>.</li> | ||
| <li>[Optional] Select best reference from <code>--mapping_constrains</code>:<ul> | ||
| <li><a href="https://github.com/marbl/Mash"><code>Mash sketch</code></a></li> | ||
| <li><a href="https://github.com/marbl/Mash"><code>Mash screen</code></a></li> | ||
|
|
@@ -1224,7 +1225,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": ".", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,7 +18,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="../images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -1337,7 +1337,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": "..", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="../assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="../assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,7 +18,7 @@ | |
|
|
||
|
|
||
| <link rel="icon" href="../images/ViralGenie-nf-core-theme.png"> | ||
| <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.18"> | ||
| <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.20"> | ||
|
|
||
|
|
||
|
|
||
|
|
@@ -2017,7 +2017,7 @@ <h3 id="preclustering-kaiju-kraken2">Preclustering - Kaiju & Kraken2</h3> | |
| <li><code>kaiju/<sample-id>_kaiju.tsv</code>: Raw output from Kaiju with taxonomic rank, read ID and taxonic ID</li> | ||
| <li><code>kraken2/<sample-id>_kraken2_reports.txt</code>: A Kraken2 report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits in the Kraken2 run for a given sample. Will be 6 column rather than 8 if <code>--save_minimizers</code> specified.</li> | ||
| <li><code>kraken2/<sample-id>_kraken2.classifiedreads.txt</code>: A list of read IDs and the hits each read had against the database for a given sample.</li> | ||
| <li><code>merged_classifications/<sample-id>_merged.tsv</code>: Taxonomy merged based on the specified strategy with the columns being taxonomic rank, read ID and taxonic ID.</li> | ||
| <li><code>merged_classifications/<sample-id>.txt</code>: Taxonomy merged based on the specified strategy, filtered based on specified filters and simplified up to a certain taxonomy with the columns being taxonomic rank, read ID and taxonic ID.</li> | ||
| <li><code>sequences/<sample-id>/<sample-id>_taxid<taxonic ID>.fa</code>: Fasta file with the contigs that were classified to that specific taxonomic ID.</li> | ||
| </ul> | ||
| </li> | ||
|
|
@@ -2877,7 +2877,7 @@ <h4>Cookie Consent</h4> | |
| <script id="__config" type="application/json">{"base": "..", "features": ["announce.dismiss", "content.action.edit", "content.code.annotate", "content.code.copy", "header.autohide", "navigation.footer", "navigation.instant", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "navigation.top", "navigation.tracking", "search.share", "search.suggest", "toc.follow"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script> | ||
|
|
||
|
|
||
| <script src="../assets/javascripts/bundle.3220b9d7.min.js"></script> | ||
| <script src="../assets/javascripts/bundle.dd8806f2.min.js"></script> | ||
|
|
||
| <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script> | ||
|
|
||
|
|
||
Oops, something went wrong.