replace all references to NeSI with REANNZ

Author: DininduSenanayake

docs/1_DesigningVariantC.md

@@ -73,10 +73,10 @@ First we need to create directories for the results that will be generated as pa
 ### Index the reference genome
 Our first step is to index the reference genome for use by BWA. Indexing allows the aligner to quickly find potential alignment sites for query sequence in a genome, which saves time during alignment. Indexing the reference only has to be run once. The only reason you would want to create a new index is if you are working with a different reference genome or you are using a different tool for alignment.
 
-Since we are working on the NeSI HPC, we need to search and load the package before we start using it.
+Since we are working on the REANNZ HPC, we need to search and load the package before we start using it.
 
 !!! key "Software as modules"
-    - Similar to other HPCs/SuperComputers, NeSI Clusters provide software as modules (this is not the only way to deploy software as it can be done via other means such as conda, containers, etc.).
+    - Similar to other HPCs/SuperComputers, REANNZ Clusters provide software as modules (this is not the only way to deploy software as it can be done via other means such as conda, containers, etc.).
     - A module is a self-contained description of a software package — it contains the settings required to run a software package and, usually, encodes required dependencies on other software packages.
     - Refer to [supplementary 1 - Accessing software via modules](https://genomicsaotearoa.github.io/Workshop-Bash_Scripting_And_HPC_Job_Scheduler/6_supplementary_1/) for more information. 
 
@@ -101,7 +101,7 @@ Since we are working on the NeSI HPC, we need to search and load the package bef
             The following modules were not unloaded:
             (Use "module --force purge" to unload all):
 
-            1) XALT/minimal   2) slurm   3) NeSI
+            1) XALT/minimal   2) slurm   
             Loaded modules BWA, SAMtools, BCFtools,HISAT2,Subread
             ```
             

docs/4_IntroductiontoHPC.md

@@ -27,9 +27,9 @@ Most HPC systems follow the ideas described above of taking many computers and l
     * The network interconnect – this dictates the communication speed between nodes. The faster this speed is, the more a group of individual nodes will act like a unit.
 
 
-### NeSI Mahuika Cluster architecture
+### REANNZ HPC cluster architecture
 
-NeSI Mahuika cluster (CRAY HPE CS400) system consists of a number of different node types. The ones visible to researchers are:
+REANNZ HPC consists of a number of different node types. The ones visible to researchers are:
 
 * Login nodes
 * Compute nodes

docs/6_supplementary_1.md

@@ -11,7 +11,7 @@ Before we start using individual software packages, however, we should understan
 
 One of the workarounds for this issue is Environment modules. A module is a self-contained description of a software package — it contains the settings required to run a software package and, usually, encodes required dependencies on other software packages.
 
-There are a number of different environment module implementations commonly used on HPC systems and the one used in NeSI Mahuika cluster is `Lmod` where the `module` command is used to interact with environment modules.
+There are a number of different environment module implementations commonly used on HPC systems and the one used in REANNZ cluster is `Lmod` where the `module` command is used to interact with environment modules.
 
 !!! circle-info "Commonly used `module` sub-commands"
 
@@ -31,7 +31,7 @@ There are a number of different environment module implementations commonly used
     ```
     * Load a specific program
 
-        - Note: All modules on NeSI have version and toolchain/environment suffixes. If none is specified, the default version for the tool is loaded. The default version can be seen with the module avail command.
+        - Note: All modules on REANNZ cluster have version and toolchain/environment suffixes. If none is specified, the default version for the tool is loaded. The default version can be seen with the module avail command.
         ```bash
         module load MY_APPLICATION
         ```

docs/index.md

@@ -38,8 +38,7 @@
 
 !!! screwdriver-wrench "Setup"
 
-    Workshop material is designed to run on NeSI Mahuika cluster via Jupyter. Instructions on how to Set/Reset Authentication factors to access NeSI Services and Jupyter Login instructions [can be found here](https://genomicsaotearoa.github.io/nesi-jupyter/)
-
+    Workshop material is designed to run on REANNZ HPC.
 <br>
 
 !!! rectangle-list "Content"