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docs: minor fixes #88

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merged 4 commits into from
Mar 6, 2024
Merged

docs: minor fixes #88

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0245a9b
docs: comments CJ
ninsch3000 Feb 1, 2024
857a2a0
Update run.py
uniqueg Mar 6, 2024
25649e7
Update README.md
uniqueg Mar 6, 2024
e9e888a
Update args.py
uniqueg Mar 6, 2024
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10 changes: 6 additions & 4 deletions README.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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/>
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2 changes: 1 addition & 1 deletion docs/guides/usage.md
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Expand Up @@ -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
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5 changes: 3 additions & 2 deletions zarp/config/args.py
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Expand Up @@ -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(
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