Merge remote-tracking branch 'origin/main' into dev

Author: alpae

README.md

@@ -53,9 +53,9 @@ any installation steps given the system supports running either docker container
 installed.
 
 ```bash
-nextflow run dessimozlab/FastOMA -profile docker --input_folder /path/to/in_folder --output_folder /path/to/out_folder
+nextflow run dessimozlab/FastOMA -profile docker  --input_folder /path/to/in_folder --output_folder /path/to/out_folder 
 ```
-
+You could also add specific version to be used by adding `-r v0.3.1` to the command line. 
 Nextflow will automatically fetch the [dessimozlab/FastOMA](https://github.com/dessimozlab/FastOMA) repository and starts 
 the `FastOMA.nf` workflow. The `-profile` argument must be used to specify the profile to use. We support `docker`, 
 `singularity` and `conda` which then automatically set up the necessary tools by downloading the required containers or creating 
@@ -91,7 +91,7 @@ The FastOMA workflow can be run directly without any installation using nextflow
 nextflow run desimozlab/FastOMA -r v0.3.1 -profile conda 
 ```
 
-This will fetch version 0.3.1 from github and run the FastOMA workflow using the conda profile. See section [How to run fastOMA](#how-to-run-fastoma). 
+This will fetch version v0.3.1 from github and run the FastOMA workflow using the conda profile. See section [How to run fastOMA](#how-to-run-fastoma). 
 
 ### 2. Cloning the FastOMA repo and running from there
 
@@ -140,7 +140,7 @@ bashMiniconda3.sh
 Then follow the instruction on the terminal. Finally, close and re-open the terminal and run
 ```
 conda create -n fastoma python=3.9 --file environment-conda.yml
-cond activate mamba activate FastOMA
+conda activate fastoma
 ```
 Then, clone and install fastOMA using
 ```
@@ -154,7 +154,7 @@ Alternatively, you could use Mamba instead of Conda (which needs its own [instal
 Note that it is not encouraged to have both Mamba and conda on one system, [more info](https://stackoverflow.com/questions/76760906/installing-mamba-on-a-machine-with-conda).
 
 ```
-mamba env create -n FastOMA -f environment_conda.yml
+mamba env create -n FastOMA -f environment-conda.yml
 mamba activate FastOMA
 ```
 
@@ -184,7 +184,7 @@ nextflow run FastOMA.nf -profile docker \
     --output_folder myresult/
 ```
 This will use the container that is tagged with the current commit id. Similarly, one could also use 
-`--container_version "0.3.1"` to use the container with version `dessimozlab/fastoma:0.3.1` from dockerhub.
+`--container_version "0.3.1"` to use the container with version `dessimozlab/fastoma:0.3.1` from dockerhub. Check the latest version on the [DockerHub](https://hub.docker.com/r/dessimozlab/fastoma/tags).
 
 ### Singularity
 Since Docker needs administrator privileges (root access), [Singluarity](https://apptainer.org/index.html) (a.k.a Apptainer) is a good alternative. This can be installed using [Conda](https://anaconda.org/conda-forge/singularity) with `conda install conda-forge::singularity`. However, in most of the academic HPC cluster, singluarity is already installed and can be called with `module load`.
@@ -449,6 +449,7 @@ Majidian, Sina, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy,
 
 
 ## Change log
+- Update  v0.3.1: spliting HOG and sampling
 - Update  v0.1.6: adding dynamic resources, additional and improved output
 - Update  v0.1.5: docker, add help, clean nextflow 
 - Update  v0.1.4: new gene families with linclust if mmseqs is installed, using quoted protein name to handle species chars, check input first