docs: add usage examples

docs/guides/examples.md

@@ -1,6 +1,36 @@
 # Examples
 
-!!! warning "Under construction"
+This section provides a growing collection of examples that demonstrate how to
+use _ZARP-cli_ in various scenarios.
 
-    This section is under preparation and will list a number of real-world,
-    fully functional examples. Please stay tuned.
+!!! info "Prerequisites"
+
+    The examples below assume that you have already [installed](./installation.md) and [initialized](./initialization.md) _ZARP-cli.
+
+## Process samples deposited to SRA
+
+Let's have ZARP-cli fetch two samples from SRA, infer all necessary metadata,
+fetch the corresponding genome annotations and start a _ZARP_ workflow run on
+them:
+
+```sh
+zarp SRR23590181 SRR23529108
+```
+
+??? tip "I want to verify the inferred metadata first!"
+
+    Set the `--execution-mode` parameter to `PREPARE_RUN` to run _ZARP-cli_ up
+    until the point of the actual _ZARP_ workflow execution:
+
+    ```sh
+    zarp --execution-mode=PREPARE_RUN SRR23590181 SRR23529108 
+    ```
+
+!!! info "More please!"
+
+    You will find a description of more elaborate use cases in the [ZARP
+    publication](https://doi.org/10.12688/f1000research.149237.1) and the
+    accompanying [supplementary materials][zarp-supplementary], published on
+    [Zenodo][zenodo]. The latter include detailed instructions, all necessary
+    input files and a selection of reference output files to validate your runs
+    against.

docs/includes/references.md

@@ -19,4 +19,6 @@
 [zarp-cli-issue-tracker]: <https://github.com/zavolanlab/zarp-cli/issues>
 [zarp-issue-tracker]: <https://github.com/zavolanlab/zarp/issues>
 [zarp-qa]: <https://github.com/zavolanlab/zarp/discussions>
-[zavolab-gh]: <https://github.com/zavolanlab>
+[zarp-supplementary]: <https://zenodo.org/records/10797372.
+[zavolab-gh]: <https://github.com/zavolanlab>
+[zenodo]: <https://zenodo.org/>