MAINT: remove genomad from the README (bokulich-lab#25)

* MAINT: remove genomad from the README

* Update installation instructions

* Update distro in the CI workflow

* Review suggestion

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
   ci:
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
-      distro: metagenome
+      distro: pathogenome
       additional-reports-path: ./coverage.xml
       additional-reports-name: coverage
 

README.md

@@ -2,45 +2,19 @@
 
 A [QIIME 2](https://qiime2.org) Plugin for detecting viral genomes and assessing their quality.
 
-###  Install development version of `q2-viromics`
-Clone the repository:
-```shell
-git clone https://github.com/bokulich-lab/q2-viromics.git
-cd q2-viromics
-```
-
-Then, run:
-
-```shell
-mamba create -n q2-viromics -c conda-forge -c bioconda -c https://packages.qiime2.org/qiime2/2024.10/metagenome/passed/ -c defaults q2cli q2-types checkv genomad pyhmmer
-```
-
-###  Activate q2-viromics environment
-```shell
-conda activate q2-viromics
-```
-
+## Installation
+_q2-viromics_ is available as part of the QIIME 2 pathogenome distribution. For installation and usage instructions please consult the official [QIIME 2 documentation](https://docs.qiime2.org). 
 
 
-### Test it out!
-#### Download sample input [datasets](https://polybox.ethz.ch/index.php/s/9jlQ4oyDWvWyvpB)
-
-Fetch the geNomad database.
-```bash
-qiime viromics genomad-fetch-db --o-database genomad_db.qza --verbose
-```
-
-Run the geNomad analysis.
-```bash
-qiime viromics genomad-analysis --i-sequences input_sequences.qza --i-database genomad_db.qza --p-num-threads 8 --p-splits 8 --output-dir genomad_output --verbose
-```
+## Usage
+Start by downloading sample input [datasets](https://polybox.ethz.ch/index.php/s/9jlQ4oyDWvWyvpB).
 
-Fetch the checkV database.
+Fetch the checkV database:
 ```bash
 qiime viromics checkv-fetch-db --o-database checkV_db.qza --verbose
 ```
 
-Run the CheckV analysis.
+Run the CheckV analysis:
 ```bash
-qiime viromics checkv-analysis --i-sequences genomad_output/viruses.qza --i-database checkV_db.qza --p-num-threads 4 --output-dir checkV_output --verbose
+qiime viromics checkv-analysis --i-sequences input_sequences.qza --i-database checkV_db.qza --p-num-threads 4 --output-dir checkV_output --verbose
 ```