structure for singularity and HPC

docs/09_reproducibility_IV.md

@@ -1,4 +1,4 @@
-# Singularity
+# Containers and the HPC
 
 ```
 Material is coming!
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          :  .-.  : :  .-.  :  '........'    (_________):  .-.  :`-'
          :  '-'  : :  '-'  :                           :  '-'  :
           '._ _.'   '._ _.'                             '._ _.'
-```
+```
+
+!!! Success "Expected Outcomes"
+  - Being able to log onto the HPC and start an interactive node
+  - Know basic HPC related commands
+  - Execute containerized code through Singularity/Apptainer
+  - Being able to search and load specific software
+  - Execute NextFlow scripts on the HPC
+
+
+## HPC: The Basics
+
+Resources:
+  - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75990696/User+Guide
+  - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75990091/HPC+High+Performance+Storage
+### Logging onto the HPC
+### Choosing the System
+### Checking Available Resources
+## Launching an Interactive Node
+
+Resources:
+  - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989825/Interactive+Jobs
+
+### SLURM and Commands
+
+Resouces:
+  - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989875/Running+Jobs+with+Slurm
+  - https://uarizona.atlassian.net/wiki/spaces/UAHPC/pages/75989486/Cheat+Sheet
+
+## Singularity/Apptainer
+### Executable Commands
+
+Resources:
+  - https://cc.cyverse.org/singularity/intro/
+  - https://cc.cyverse.org/singularity/hpc/
+  - https://cc.cyverse.org/singularity/advanced/
+
+## NextFlow on the HPC
+
+Resources:
+- https://training.nextflow.io/basic_training/executors/
+- https://lescailab.unipv.it/guides/eos_guide/use_nextflow.html
+- Example: https://nf-co.re/smartseq2/dev/docs/usage