minor fixes

AustralianBioCommons · Sep 9, 2024 · 86a662a · 86a662a
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diff --git a/assets/doc_img/login.png b/assets/doc_img/login.png
diff --git a/index.md b/index.md
@@ -3,6 +3,13 @@ title: The Australian Nextflow Seqera Service
 toc: false
 ---
 
+# About the service
+
+The Australian Nextflow Seqera Service is a centralised web platform for managing, launching and monitoring the execution of Nextflow bioinformatics pipelines on [Seqera-compatible compute environments](https://docs.seqera.io/platform/latest/compute-envs/overview). Australian research organisations and individual researchers can add compute infrastructure they have access to and publish pipelines to private or shared workspaces to run data analyses at scale. The service provides access to all features available through the [Seqera Platform](https://seqera.io/platform/) including data exploration and analysis as well as notebook analysis.
+
+# Operational Partners
+
+[Australian BioCommons](https://www.biocommons.org.au/) (whose lead agent is the University of Melbourne) operates the Australian Nextflow Seqera Service in collaboration with [Pawsey Supercomputing Research Centre](https://pawsey.org.au/), [National Computational Infrastructure (NCI)](https://nci.org.au/), and [Seqera](https://seqera.io/). The Service was established as an output of the Australian BioCommons [Bring Your Own Data Expansion Project](https://www.biocommons.org.au/byo-data-platform-expansion) and is hosted on Amazon Web Services (AWS). It is supported by [Bioplatforms Australia](https://www.bioplatforms.com/) via [NCRIS funding](https://www.education.gov.au/ncris).
 
 
 <br />  

diff --git a/main/pilot-project.md b/main/pilot-project.md
@@ -55,6 +55,7 @@ Since investigations commenced in July 2022 till the end of the pilot project in
 <br />
 
 ## Participants of the pilot project
+
 <div class="container">
     <div class="row">
         <div class="col-sm-3" style="border: 1px solid; box-shadow: 3px 3px 3px 3px #888888; padding: 10px; margin: 20px" >
@@ -196,6 +197,8 @@ Since investigations commenced in July 2022 till the end of the pilot project in
 
 <br />  
 
+## Acknowledgements
+
 <br />  
 
 {% include affiliation-tiles-selection.html type="support" %}
diff --git a/main/service-commitments.md b/main/service-commitments.md
@@ -222,8 +222,3 @@ Updates on the status of these backends are available at:
 
 - <a href="https://status.pawsey.org.au/"> Setonix Status</a>
 - <a href="https://nci.org.au/our-systems/status"> GADI Status</a>
-
-
-
-# Communicating changes to the service
-Changes to the Australian Nextflow Seqera Services including version upgrades, networking changes and others need to be communicated to all Australian BioCommons Service Contacttional partners, compute providers and users. All these changes should be communicated to the Australian BioCommons Service Contact and they will communicate this information to all relevant Operational Partners.
diff --git a/main/service-terms.md b/main/service-terms.md
@@ -3,15 +3,13 @@ title: Terms of service
 toc: true
 ---
 
-# About the service
-
-The Australian Nextflow Seqera Service is a centralised web platform for managing, launching and monitoring the execution of Nextflow bioinformatics pipelines on [Seqera-compatible compute environments](https://docs.seqera.io/platform/latest/compute-envs/overview). Australian research organisations and individual researchers can add compute infrastructure they have access to and publish pipelines to private or shared workspaces to run data analyses at scale. The service provides access to all features available through the [Seqera Platform](https://seqera.io/platform/) including data exploration and analysis as well as notebook analysis.
+# Definitions
 
 ## Operational Partners
 
 [Australian BioCommons](https://www.biocommons.org.au/) (whose lead agent is the University of Melbourne) operates the Australian Nextflow Seqera Service in collaboration with [Pawsey Supercomputing Research Centre](https://pawsey.org.au/), [National Computational Infrastructure (NCI)](https://nci.org.au/), and [Seqera](https://seqera.io/). The Service was established as an output of the Australian BioCommons [Bring Your Own Data Expansion Project](https://www.biocommons.org.au/byo-data-platform-expansion) and is hosted on Amazon Web Services (AWS). It is supported by [Bioplatforms Australia](https://www.bioplatforms.com/) via [NCRIS funding](https://www.education.gov.au/ncris).
 
-## Definition: Australian Research Organisation
+## Australian Research Organisation
 
 For the purposes of these terms of service, an Australian Research Organisation is defined as: A research group within a recognised Australian academic or research institute, or a research consortium receiving Australian research funding.
 

diff --git a/user-guide/compute-env.md b/user-guide/compute-env.md
@@ -74,7 +74,7 @@ The following steps need to be completed in order unless they have been complete
         </h2>
         <div id="collapse-tower-agent" class="accordion-collapse collapse" aria-labelledby="heading-tower-agent" data-bs-parent="#accordion-comp-env-all">
           <div class="accordion-body">
-            <p><a href="https://docs.seqera.io/platform/latest/agent/">Tower Agent</a> is software that runs on the HPC and communicates with the Seqera API to perform all tasks needed on the HPC, including launching a pipeline and monitoring its execution. For an admin to create a tower agent credential, follow these steps:</p>
+            <p><a href="https://docs.seqera.io/platform/latest/credentials/agent_credentials">Tower Agent</a> is software that runs on the HPC and communicates with the Seqera API to perform all tasks needed on the HPC, including launching a pipeline and monitoring its execution. For an admin to create a tower agent credential, follow these steps:</p>
             <ol>
                 <li>Navigate to the workspace you want to add credentials to, then click on the <code>Credentials</code> tab.</li>
                 <li>Click on the <code>Add Credentials</code> button under <code>Credentials</code> to create a shared <code>Agent connection ID</code> for the Tower Agent.</li>
@@ -99,7 +99,7 @@ The following steps need to be completed in order unless they have been complete
                     </ol>
                 </li>
             </ol>
-            <p>The steps above will help to create the credentials and understand the Agent&rsquo;s parameters and how it runs. In practice, this can be better optimised by having all scripts and tokens in config files and bash scripts. See [best practice recommendations]((/user-guide/hpc-recommendations). The procedure is also described in the Seqera documentation at <a href="https://docs.seqera.io/platform/latest/agent/#quickstart">Quick Start</a>.</p>
+            <p>The steps above will help to create the credentials and understand the Agent&rsquo;s parameters and how it runs. In practice, this can be better optimised by having all scripts and tokens in config files and bash scripts. See [best practice recommendations](/user-guide/hpc-recommendations). The procedure is also described in the Seqera documentation at <a href="https://docs.seqera.io/platform/latest/credentials/agent_credentials">Quick Start</a>.</p>
             <div class="alert alert-primary" role="alert">
             <h4 class="alert-heading">Note</h4>
             <p>Users of the same workspace share credentials, so there is no need to create a credential per user within a workspace.</p>
@@ -138,7 +138,7 @@ The following steps need to be completed in order unless they have been complete
                 </li>
                 <li>Select workdirectory 
                     <ul>
-                        <li>This can remain as $TW_AGENT_WORK or specify your own</li>
+                        <li>This can remain as <code>$TW_AGENT_WORK</code> or specify your own</li>
                     </ul>
                 </li>
                 <li>Leave the launch directory field empty.</li>

diff --git a/user-guide/hpc-recommendations.md b/user-guide/hpc-recommendations.md
@@ -12,6 +12,3 @@ page_id: pg-5
 1. Make sure that the working directory of the Agent is not used as a working directory by other users. This can cause access permission issues.
 2. Consider running the Agent in the background or using jobs on the HPC, so you don’t need to start the Agent very often.
 
-## Recommendations on configuring compute environments on Setonix at Pawsey.
-
-## Recommendations on configuring compute environments on GADI at NCI.