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authorPeter Amstutz2020-08-05 16:06:11 -0400
committerGitHub2020-08-05 16:06:11 -0400
commitfdb1b012fc04ee07f401541e181e28fe442c9454 (patch)
tree8486db1087692dffcea9d93814e436d9cf150b47 /doc/blog/using-covid-19-pubseq-part2.org
parent86f31ef60f65a820bf9ac25c3fc01c88f2a9ebfe (diff)
parent2d20bf90497588a297ca98a78ee0fbbcadf95569 (diff)
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Merge pull request #99 from AndreaGuarracino/patch-2
several fixes in the website, added links to video talk and poster, new pangenome generation workflow
Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part2.org')
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diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org
index d2a1cbc..349fd06 100644
--- a/doc/blog/using-covid-19-pubseq-part2.org
+++ b/doc/blog/using-covid-19-pubseq-part2.org
@@ -8,36 +8,13 @@
#+HTML_LINK_HOME: http://covid19.genenetwork.org
#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
-As part of the COVID-19 Biohackathon 2020 we formed a working group to
-create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
-Corona virus sequences. The general idea is to create a repository
-that has a low barrier to entry for uploading sequence data using best
-practices. I.e., data published with a creative commons 4.0 (CC-4.0)
-license with metadata using state-of-the art standards and, perhaps
-most importantly, providing standardised workflows that get triggered
-on upload, so that results are immediately available in standardised
-data formats.
-
* Table of Contents :TOC:noexport:
- [[#finding-output-of-workflows][Finding output of workflows]]
- - [[#introduction][Introduction]]
- [[#the-arvados-file-interface][The Arvados file interface]]
- [[#using-the-arvados-api][Using the Arvados API]]
* Finding output of workflows
-As part of the COVID-19 Biohackathon 2020 we formed a working group to
-create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
-Corona virus sequences. The general idea is to create a repository
-that has a low barrier to entry for uploading sequence data using best
-practices. I.e., data published with a creative commons 4.0 (CC-4.0)
-license with metadata using state-of-the art standards and, perhaps
-most importantly, providing standardised workflows that get triggered
-on upload, so that results are immediately available in standardised
-data formats.
-
-* Introduction
-
We are using Arvados to run common workflow language (CWL) pipelines.
The most recent output is on display on a [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][web page]] (with time stamp)
and a full list is generated [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. It is nice to start up, but for
@@ -81,4 +58,4 @@ its listed UUID:
: arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839de18290843a@5ed7f3c5
-* Using the Arvados API
+* TODO Using the Arvados API