docs: updated software list

includes/data/software.yml

@@ -4798,7 +4798,7 @@ software_modules:
           checks on raw sequence data coming from high throughput sequencing pipelines.,
         markedDefault: false, versionName: 0.11.8}
     - categories: biology, genomics
-      defaultVersionName: 0.7.0
+      defaultVersionName: 0.7.1
       description: Dorado is a high-performance, easy-to-use, open source basecaller
         for Oxford Nanopore reads.
       package: dorado
@@ -4809,7 +4809,7 @@ software_modules:
       - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
           for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3}
       - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
-          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.0}
+          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.1}
     - categories: biology, genomics
       defaultVersionName: 0.44.0
       description: kallisto is a program for quantifying abundances of transcripts

src/docs/software/updates.xml

@@ -14,15 +14,6 @@
         <author>[email protected] (Kilian Cavalotti)</author>
         <pubDate>Wed, 29 May 2024 09:16:34 -0700</pubDate>
     </item>
-    <item>
-        <title>New version: biology/dorado version 0.7.0</title>
-        <description>Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.</description>
-        <link>https://github.com/nanoporetech/dorado</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.7.0#dorado</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Fri, 24 May 2024 10:51:36 -0700</pubDate>
-    </item>
     <item>
         <title>New version: system/gh version 2.49.2</title>
         <description>gh is GitHub on the command line. It brings pull requests, issues, and other GitHub concepts to the terminal next to where you are already working with git and your code.</description>
@@ -446,24 +437,6 @@
         <author>[email protected] (Kilian Cavalotti)</author>
         <pubDate>Fri, 22 Mar 2024 18:43:21 -0700</pubDate>
     </item>
-    <item>
-        <title>New version: math/cudnn version 9.0.0.312</title>
-        <description>NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks.</description>
-        <link>https://developer.nvidia.com/cudnn</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=9.0.0.312#cudnn</guid>
-        <category>math, deep learning</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Fri, 22 Mar 2024 17:21:35 -0700</pubDate>
-    </item>
-    <item>
-        <title>New version: biology/salmon version 1.10.0</title>
-        <description>Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.</description>
-        <link>https://combine-lab.github.io/salmon</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.10.0#salmon</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Wed, 6 Mar 2024 14:17:16 -0800</pubDate>
-    </item>
     <item>
         <title>Removed version: system/google-cloud-sdk version 338.0.0</title>
         <description>google-cloud-sdk/338.0.0</description>