updated docs

docs/examples.md

@@ -1,19 +1,41 @@
+## Download tables 
+
+Starting from version `0.8.0`, you can restrict outputs to `assembly_summary.tsv` and `taxonomy.tsv`
+
+* Command
+
+```sh
+assembly_finder -i staphylococcus_aureus -nb 1 --summary
+```
+
+* Output
+
+```sh
+📂staphylococcus_aureus
+ ┣ 📂logs
+ ┃ ┣ 📂taxons
+ ┃ ┃ ┗ 📜staphylococcus_aureus.log
+ ┃ ┗📜lineage.log
+ ┣ 📜assembly_finder.log
+ ┣ 📜assembly_summary.tsv
+ ┣ 📜config.yaml
+ ┗ 📜taxonomy.tsv
+```
+
 ## Download genomes
 ### Small datasets
 * *Staphylococcus aureus* reference genome
 
-
-!!! note
-    By default, assembly_finder limits genomes to reference or representative
-
 ```sh
 assembly_finder -i staphylococcus_aureus -nb 1
 ```
+!!! note
+    By default, assembly_finder limits genomes to reference or representative
 
 * Any *Staphylococcus aureus* genome
 
 ```sh
-assembly_finder -i staphylococcus_aureus -nb 1 --reference False
+assembly_finder -i staphylococcus_aureus -nb 1 --reference false
 ```
 
 * Download from a list of taxa
@@ -58,7 +80,9 @@ assembly_finder -i bacteria --api-key <api-key> --rank species --nrank 1
 * Complete RefSeq bacteria viruses and archaea <small>(excluding MAGs and atypical)</small>
 
 ```sh
-assembly_finder -i bacteria,viruses,archaea -o outdir --api-key <api-key> --source refseq --assembly-level complete --mag exclude --atypical
+assembly_finder -i bacteria,viruses,archaea --api-key <api-key> \
+--source refseq --assembly-level complete --mag exclude --atypical \
+-o outdir
 ```
 
 * Specific bioproject
@@ -68,7 +92,8 @@ assembly_finder -i PRJNA289059 --api-key <api-key> --accession
 ```
 ## Download other files <small>(cds, proteins, gff3 ...)</small>
 ```sh
-assembly_finder -i staphylococcus_aureus -nb 1 --include genome,rna,protein,cds,gff3,gtf,gbff,seq-report
+assembly_finder -i staphylococcus_aureus -nb 1 \
+--include genome,rna,protein,cds,gff3,gtf,gbff,seq-report
 ```
 Output:
 ```sh
@@ -81,6 +106,7 @@ Output:
  ┃ ┃ ┣ 📜genomic.gff.gz
  ┃ ┃ ┣ 📜genomic.gtf.gz
  ┃ ┃ ┗ 📜protein.faa.gz
+ ┃ ┃ ┗ 📜sequence_report.jsonl 
  ┃ ┗ 📜.snakemake_timestamp
  ┣ 📂logs
  ┃ ┣ 📂taxons
@@ -93,6 +119,5 @@ Output:
  ┣ 📜assembly_finder.log
  ┣ 📜assembly_summary.tsv
  ┣ 📜config.yaml
- ┣ 📜sequence_report.tsv
  ┗ 📜taxonomy.tsv
 ```

docs/index.md

@@ -1,14 +1,16 @@
-# Assembly Finder
+# assembly_finder
+[![tests](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml)
+[![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml)
+[![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml)
 
 [![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool)
 [![license](https://img.shields.io/github/license/metagenlab/assembly_finder.svg)](https://github.com/metagenlab/assembly_finder/blob/main/LICENSE)
-[![version](https://img.shields.io/conda/v/bioconda/assembly_finder?label=version)](http://bioconda.github.io/recipes/assembly_finder/README.html)
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/assembly_finder/README.html)
+[![version](https://img.shields.io/conda/vn/bioconda/assembly_finder)](http://bioconda.github.io/recipes/assembly_finder/README.html)
 [![downloads](https://img.shields.io/conda/dn/bioconda/assembly_finder)](https://anaconda.org/bioconda/assembly_finder)
-[![tests](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml)
-[![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml)
 
-Assembly finder is a Snakemake-powered cli to download genomes with [NCBI datasets](https://github.com/ncbi/datasets).
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13353494.svg)](https://zenodo.org/doi/10.5281/zenodo.13353494)
+
+assembly_finder is a [Snakemake](https://github.com/snakemake/snakemake)-powered cli to download genomes with [NCBI datasets](https://github.com/ncbi/datasets).  
 
 ## Installation
 
@@ -18,7 +20,7 @@ Assembly finder is a Snakemake-powered cli to download genomes with [NCBI datase
     mamba create -n assembly_finder assembly_finder
     ```
     !!! note
-        Requires a [mamba](https://github.com/conda-forge/miniforge) installation
+        Requires a [Miniforge](https://github.com/conda-forge/miniforge) installation
 === "docker" 
 
     ```sh
@@ -35,7 +37,7 @@ Assembly finder is a Snakemake-powered cli to download genomes with [NCBI datase
     pip install -e assembly_finder
     ```
     !!! note
-        Requires a [mamba](https://github.com/conda-forge/miniforge) installation
+        Requires a [Miniforge](https://github.com/conda-forge/miniforge) installation
 
 ## Usage 
 ### Command
@@ -71,7 +73,6 @@ Assembly finder is a Snakemake-powered cli to download genomes with [NCBI datase
  ┣ 📜assembly_finder.log
  ┣ 📜assembly_summary.tsv
  ┣ 📜config.yaml
- ┣ 📜sequence_report.tsv
  ┗ 📜taxonomy.tsv
 ```
 

docs/inputs.md

@@ -6,40 +6,47 @@ Input can be either a string or a table, and queries can be either taxa or acces
 
 === "Taxons"
 
-    !!! note
-
-        Taxons can be either taxids or taxon names
-
     ```sh
     assembly_finder -i 1290,staphylococcus_aureus,562 -nb 1 -o taxons
     ```
+
+    !!! note
+
+        Taxons can be either taxids or taxon names
 
 === "Accessions"
 
     ```sh
-    assembly_finder --accession -i GCF_003812505.1,GCF_000418345.1,GCF_000157115.2 -o accessions
+    assembly_finder --accession -i GCF_003812505.1,\
+    GCF_000418345.1,GCF_000157115.2 -o accessions
     ```
+    !!! note
+
+        Accessions can be bioproject or genome accessions see [ncbi-datasets docs](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/get-genome-metadata/)
 
 ## Tables
 
 === "Taxons"
 
-    !!! note
-        You can set the number of genomes per taxon in the table
-
     | taxon | nb |
     | :-------------------- | :-- |
     | 1290 | 1 |
     | staphylococcus_aureus | 1 |
     | 562 | 1 |
 
+    !!! note
+
+        You can set the number of genomes per taxon in the table
+
 === "Accessions"
 
-    !!! note
 
-        The accession table does not have a header
 
     | GCF_003812505.1 |
     | :-------------- |
     | GCF_000418345.1 |
     | GCF_000157115.2 |
+
+    !!! note
+
+        The accession table does not have a header