docs: minor fixes (#88)

Co-authored-by: Christina Herrmann <christina.herrmann@unibas.ch>

Author: uniqueg

README.md

@@ -17,10 +17,11 @@ where to start? **Easy - _ZARP 'em!_**
 - Barry left you some samples to analyze and then went on vacation, again? **No
 problem, _ZARP 'em!_**  
 
-ZARP-cli uses the HTSinfer package to infer missing metadata and then runs the
-[ZARP RNA-Seq analysis pipeline][zarp] on your samples. Impress your colleagues
-with your sudden productivity boost. Or better yet, use the time saved to go on
-that camping trip with Barry. Just make sure to guard your secret! :wink:
+ZARP-cli uses the [HTSinfer][htsinfer] package to infer missing metadata and
+then runs the [ZARP RNA-Seq analysis pipeline][zarp] on your samples. Impress
+your colleagueswith your sudden productivity boost. Or better yet, use the time
+saved to go on that camping trip with Barry. Just make sure to guard your
+secret! :wink:
 
 ## Basic usage
 
@@ -112,6 +113,7 @@ by [email][contact].
 [badge-url-docs]: <https://zavolanlab.github.io/zarp-cli>
 [badge-url-github-tag]: <https://github.com/zavolanlab/zarp-cli/releases>
 [badge-url-license]: <http://www.apache.org/licenses/LICENSE-2.0>
+[htsinfer]: <https://github.com/zavolanlab/htsinfer>
 [issue-tracker]: <https://github.com/zavolanlab/zarp-cli/issues>
 [mamba]: <https://github.com/mamba-org/mamba>
 [semver]: <https://semver.org/>

docs/guides/usage.md

@@ -47,7 +47,7 @@ Available command-line parameters are grouped into the following sections:
 | **Run modes** | These parameters execute _ZARP-cli_ in special modes, e.g., for initialization or to display the help screen |
 | **Sample-specific** | These parameters modify globally set metadata for all samples of a run, unless overridden inside provided sample tables |
 | **Run-specific** | These parameters modify the behavior of _ZARP-cli_ or set metadata to describe runs |
-| **User-specific** | These parameters that will be included in the _ZARP_ report, if available |
+| **User-specific** | These parameters will be included in the _ZARP_ report, if available |
 
 A complete listing of all available CLI options can easily be printed to the
 screen, together with detailed descriptions, with the following command and

zarp/config/args.py

@@ -405,8 +405,9 @@ def _set_run_arguments(
             default=None,
             type=str,
             help=(
-                "run identifier; if not provided a random string will be"
-                " generated"
+                "whether to trigger a full ZARP-cli run, "
+                "a dry run (external tools are not run, for testing),"
+                "or prepare a ZARP run (input data creation only)"
             ),
         )
         argument_group.add_argument(