glossary.yml

Shell: |
  A command processor that we interact with via the system prompt. In our case, the Shell we're interacting with is on the server.

executable: |
  Software that is runnable on a system. Some of these are built in, such as `wc`, but most we will need to load or install into our system.

bash: |
  Short for *Bourne* *Again* *Shell* - it is the command processor that is typically run in a text window, has its own programming language and syntax.

Terminal: |
  The program on our own machine that we use to interact with a shell (usually on a remote machine)

Directory: |
  A container in which we save files. Can be nested (that is, have a directory inside a directory)
  
metadata: |
  Information about a file or dataset, such as the filename, or date created. 
  
"batch jobs": |
  Running the same task on a group of files. Can be done locally (on your computer) or on a cluster.

"batch processing": |
  A way to automate processing a number of files. For example, we might have a folder of .bam files and want to check the counts on each of them.

cluster: |
  A networked group of computers. Usually contains a driver node and compute nodes.

"Compute Job": |
  A task that we have assigned a computer to run. This computer can be a compute node in a cluster, or our own machine.

subjob: |
  A task that has a parent task. Usually a subjob = 1 node processing.

Registry: |
  collection of repositories that you pull docker images from. Example repositories include DockerHub and Quay.io.
  
Image: |
  what you download from a registry - the "recipe" for building the software environment. Stored in a registry. use `apptainer pull` to get image from a registry. Can also generate image from a Dockerfile

Container: | 
  The executable software environment actually installed and running on a machine. Runnable. Generate from `docker pull` from a repository.

"Snapshot File": | 
  An single archive file (`.tar.gz`) that contains the Docker container. Generate using `docker save` on a container.  Also known as an *image file*. 

Dockerfile: | 
  A file that specifies how to install software and its dependencies. You often base a Dockerfile on an existing Docker image

Tag: | 
  A bit of metadata that is used to *version* a container. 

workflow: |
  A way to process files through a sequence of steps. Also known as a pipeline.
  
"workflow manager": |
  A system that works with the cluster manager to orchestrate processing data through a workflow
  
WDL: |
  Short for Workflow Description Language. A standard for specifying a workflow, which includes describing inputs, saving intermediate outputs, and outputting processed files.

Docker: |
  Software that builds and runs containers

DockerHub: |
  A site to host your docker images. Your images can be private or public.

ephemeral: |
  When you are finished with Docker containers, everything that you created in them will disappear when you finish running scripts in the container.

Apptainer: |
  A container software that is often used on HPC systems. Can run Docker containers.

Cromwell: |
  A workflow runner. Currently works with WDL files.

Sprocket: |
  A newer workflow runner that works with WDL files. 

"HPC": |
  Short for High Performance Computing. See the hpc basics chapter for more info.

SLURM: |
  "Simple Linux Utility for Resource Management" - it handles scheduling and distributing jobs among the compute nodes in the cluster.

glob: |
  a pattern-matching mechanism used primarily in shells (like Bash) and various programming languages to match filenames and paths. It is also known as "filename expansion" or "wildcard matching."

"Application Program Interface": |
  Also known as an API. The public way to interact with a webservice or software app.

"job array": |
  A numbered list that usually goes from 1 to the length of the list. Used in SLURM batch processing.