Glossary
Terms used in the lessons, in one line each
| Term | Meaning | Lesson |
|---|---|---|
| Bind mount | Making a folder of your computer visible inside a container (-v "$PWD":/work). |
08 |
| Bioconda | A conda channel of bioinformatics software. | 05 |
| Branch | A separate line of work in a Git repository. | 04 |
| CARE | Collective benefit, Authority to control, Responsibility, Ethics: principles for data from Indigenous Peoples, used together with FAIR. | 03 |
| Cell (code cell) | A block of code in a Quarto document or notebook that runs when the document renders. | 07 |
| Channel (conda) | A place packages are downloaded from, such as conda-forge or bioconda. | 05 |
| Channel (Nextflow) | A queue of data items connecting processes. | 10 |
| Checksum | A short fingerprint of a file (md5, SHA-256); any change to the file changes it. | 03 |
| CI (continuous integration) | Automatic checks that run on every push, here with GitHub Actions. | 04 |
CITATION.cff |
A file that says how to cite a repository; GitHub and Zenodo read it. | 11 |
| Commit | A recorded snapshot of a Git repository, with a message. | 04 |
| conda-forge | The largest community conda channel, for general software. | 05 |
| Container / image | An image packs software and a minimal operating system; a container is a running image. | 08 |
| Digest | The checksum of a container image (@sha256:...); unlike a tag it never changes. |
08 |
| DOI | A persistent identifier for a publication, dataset or software release. | 12 |
| Environment | The software (programs and libraries, with versions) an analysis runs with. | 05 |
| FAIR | Findable, Accessible, Interoperable, Reusable: principles for data. | 03 |
| Feature (Pixi) | A named set of dependencies, tasks and platforms that environments are built from. | 05 |
| Job graph (DAG) | The jobs of a workflow and the files that connect them. | 09 |
| Literate programming | Text and code in one document, rendered by running the code. | 07 |
Lock file (pixi.lock) |
The exact package files and checksums of an environment, for every platform. | 05 |
Manifest (pixi.toml) |
What software a project asks for, written by you. | 05 |
| Metadata | Data about the data: where it comes from, what each column and file means. | 03 |
| Process (Nextflow) | A step of a Nextflow pipeline: inputs, outputs, script. | 10 |
| Pull request | A proposal to merge a branch, with review and checks. | 04 |
| Recipe (conda) | Instructions to build a conda package: source, requirements, tests, license. | Package and share your tool |
| Replicable | A new study with new data gives consistent results. | 01a |
| Reproducible | The same data and the same analysis give the same results. | 01a |
| Rule (Snakemake) | How to make output files from input files. | 09 |
| Task (Pixi) | A named command in pixi.toml, run with pixi run NAME. |
05 |
| Template | A ready-made project layout generated with one command (Cookiecutter). | 02 |
| Wildcard | A placeholder in a Snakemake file name ({sample}) filled in from the requested file. |
09 |
| Workflow manager | A tool that runs the steps of an analysis in the right order, only when needed. | 09 |