diff options
Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part2.org')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part2.org | 25 |
1 files changed, 1 insertions, 24 deletions
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 |