MAINT: update README

README.md

@@ -1,6 +1,46 @@
 # q2-moshpit
 ![CI](https://github.com/bokulich-lab/q2-moshpit/actions/workflows/ci.yaml/badge.svg)
-![QIIME CI](https://github.com/bokulich-lab/q2-moshpit/actions/workflows/q2-ci.yaml/badge.svg)
 [![codecov](https://codecov.io/gh/bokulich-lab/q2-moshpit/graph/badge.svg?token=PSCAYJUP01)](https://codecov.io/gh/bokulich-lab/q2-moshpit)
 
 **MO**dular **SH**otgun metagenome **P**ipelines with **I**ntegrated provenance **T**racking
+QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes.
+
+## Installation
+_q2-moshpit_ is available as part of the QIIME 2 metagenome distribution. For installation and usage instructions please consult the official [QIIME 2 documentation](https://www.docs.qiime2.org). 
+
+## Functionality
+This QIIME 2 plugin contains actions used to annotate and classify (meta)genomes.
+Below you will find an overview of actions available in the plugin.
+
+| Action               | Description                                                | Underlying tool                                                    |
+|----------------------|------------------------------------------------------------|--------------------------------------------------------------------|
+| bin-contigs-metabat  | Bin contigs into MAGs using MetaBat 2.                     | [MetaBat 2](https://bitbucket.org/berkeleylab/metabat/src/master/) |
+| build-custom-diamond-db | Create a DIAMOND reference database from a FASTA input file. | [Diamond](https://github.com/bbuchfink/diamond) |
+| build-eggnog-diamond-db | Create a DIAMOND reference database for the specified taxon. | [Diamond](https://github.com/bbuchfink/diamond) |
+| build-kraken-db      | Fetch an existing or build a custom Kraken 2 database.     | [Kraken 2](https://ccb.jhu.edu/software/kraken2/)                  |
+| classify-kaiju | Classify reads using Kaiju. | [Kaiju](https://bioinformatics-centre.github.io/kaiju/) |
+| classify-kraken2      | Classify reads/MAGs using Kraken 2.                        | [Kraken 2](https://ccb.jhu.edu/software/kraken2/)                  |
+| dereplicate-mags | Dereplicate MAGs from multiple samples. | - |
+| eggnog-annotate          | Annotate orthologs against eggNOG database. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| eggnog-diamond-search    | Run eggNOG search using diamond aligner. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| eggnog-hmmer-search      | Run eggNOG search using HMMER aligner. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| estimate-bracken         | Perform read abundance re-estimation using Bracken. | [Kraken 2](https://ccb.jhu.edu/software/bracken/) |
+| estimate-mag-abundance   | Estimate MAG abundance. | - | 
+| evaluate-busco           | Evaluate quality of the generated MAGs using BUSCO. | [BUSCO](https://busco.ezlab.org) |
+| extract-annotations      | Extract annotation frequencies from all annotations. | - |
+| fetch-busco-db           | Download BUSCO database. | [BUSCO](https://busco.ezlab.org) |
+| fetch-diamond-db         | Fetch the complete Diamond database necessary to run the eggnog-diamond-search action. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| fetch-eggnog-db          | Fetch the databases necessary to run the eggnog-annotate action. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| fetch-eggnog-hmmer-db    | Fetch the taxon specific database necessary to run the eggnog-hmmer-search action. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| fetch-eggnog-proteins    | Fetch the databases necessary to run the build-eggnog-diamond-db action. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| fetch-kaiju-db           | Fetch Kaiju database. | [Kaiju](https://bioinformatics-centre.github.io/kaiju/) |
+| fetch-ncbi-taxonomy      | Fetch NCBI reference taxonomy. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
+| filter-derep-mags        | Filter dereplicated MAGs. | - |
+| filter-mags              | Filter MAGs. | - |
+| filter-reads-pangenome   | Remove contaminating human reads. | [Bowtie 2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml) |
+| get-feature-lengths      | Get feature lengths. | - |
+| inspect-kraken2-db       | Inspect a Kraken 2 database. |
+| kraken2-to-features      | Select downstream features from Kraken 2. | - |
+| kraken2-to-mag-features  | Select downstream MAG features from Kraken 2. | - |
+| multiply-tables          | Multiply two feature tables. | - |
+| predict-genes-prodigal   | Predict gene sequences from MAGs using Prodigal. | [Prodigal](https://github.com/hyattpd/Prodigal) |

environment-files/q2-moshpit-qiime2-metagenome-2024.10.yml

@@ -0,0 +1,10 @@
+channels:
+- https://packages.qiime2.org/qiime2/2024.10/metagenome/passed
+- conda-forge
+- bioconda
+dependencies:
+  - qiime2-metagenome
+  - pip
+  - pip:
+    - q2-moshpit@git+https://github.com/bokulich-lab/q2-moshpit.git@main
+