chore!: supporting only snakemake >=8.24.1 (#130)

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

README.md

@@ -1,7 +1,7 @@
 # Snakemake workflow: MPRAsnakeflow
 
 [![Documentation Status](https://readthedocs.org/projects/mprasnakeflow/badge/?version=latest)](https://mprasnakeflow.readthedocs.io/latest/?badge=latest)
-[![Snakemake](https://img.shields.io/badge/snakemake-≥7.2.1-brightgreen.svg)](https://snakemake.bitbucket.io)
+[![Snakemake](https://img.shields.io/badge/snakemake-≥8.24.1-brightgreen.svg)](https://snakemake.github.io/)
 [![Tests](https://github.com/kircherlab/MPRAsnakeflow/actions/workflows/main.yml/badge.svg)](https://github.com/kircherlab/MPRAsnakeflow/actions/workflows/main.yml)
 
 This pipeline processes sequencing data from Massively Parallel Reporter Assays (MPRA) to create count tables for candidate sequences tested in the experiment.
@@ -33,17 +33,17 @@ Create or adjust the `config/example_config.yaml` in the repository to your need
 
 ### Step 3: Install Snakemake
 
-Install Snakemake (recommended version >= 8.x) using [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) or [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) (recommended installation via [miniforge](https://github.com/conda-forge/miniforge)):
+Install Snakemake (version >= 8.24.1) using [conda >24.7.1](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) (recommended installation via [miniforge](https://github.com/conda-forge/miniforge)):
 
-    mamba create -c bioconda -n snakemake snakemake
+    conda create -c bioconda -n snakemake snakemake
 
 For installation details, see the [instructions in the Snakemake documentation](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html).
 
 ### Step 4: Execute workflow
 
 Activate the conda environment:
 
-    mamba activate snakemake
+    conda activate snakemake
 
 Test your configuration by performing a dry-run via
 
@@ -58,9 +58,6 @@ using `$N` cores or run it in a cluster environment (here SLURM) via the [slurm
     snakemake --software-deployment-method conda --executor slurm --cores $N --configfile config.yaml --workflow-profile profiles/default
 
 Please note that `profiles/default/config.yaml` has to be adapted to your needs (like partition names).
-For snakemake 7.x this might work too using slurm sbatch (but depricated in newer snakemake versions:
-
-    snakemake --use-conda --configfile config.yaml --cluster "sbatch --nodes=1 --ntasks={cluster.threads} --mem={cluster.mem} -t {cluster.time} -p {cluster.queue} -o {cluster.output}" --jobs 100 --cluster-config config/sbatch.yaml
 
 
 Please note that the log folder of the cluster environment has to be generated first, e.g:

docs/cluster.rst

@@ -32,10 +32,10 @@ Using the slurm excecutor plugin running 300 jobs in parallel.
     snakemake --sdm conda --configfile config/config.yaml -j 300  --workflow-profile profiles/default --executor slurm
 
 
-Snakemake 7
------------
+Snakemake 7 (not supported anymore)
+-------------------------------------
 
-Here we used the :code:`--cluster` option which is not anymo,onger available in snakemake 8. You can also use the predefined `config/sbatch.yaml` but this might be outdated and we highly recommend to use resources with the workfloe profile. 
+Here we used the :code:`--cluster` option which is not available in snakemake 8. You can also use the predefined `config/sbatch.yaml` but this might be outdated and we highly recommend to use resources with the workfloe profile. 
 
 .. code-block:: bash
 

docs/contributing.rst

@@ -129,8 +129,8 @@ Use the following steps for installing Sphinx and the dependencies for building
 .. code-block:: bash
 
     cd MPRAsnakeflow/docs
-    mamba env create -f environment.yml -n sphinx
-    mamba activate sphinx
+    conda env create -f environment.yml -n sphinx
+    conda activate sphinx
 
 Use the following for building the documentation.
 The first two lines is only required for loading the virtualenv.

docs/index.rst

@@ -4,19 +4,19 @@
 MPRAsnakeflow's documentation
 ====================================
 
-.. image:: https://img.shields.io/badge/snakemake-≥7.7.1-brightgreen.svg
-    :target: https://snakemake.bitbucket.io
+.. image:: https://img.shields.io/badge/snakemake-≥8.24.1-brightgreen.svg
+    :target: https://snakemake.github.io/
 
-.. image:: https://img.shields.io/badge/mamba-≥4.6-brightgreen.svg
-    :target: https://docs.conda.io/en/latest/miniconda.html
+.. image:: https://img.shields.io/badge/conda->24.7.1-brightgreen.svg
+    :target: https://github.com/conda-forge/miniforge
 
 
 **Welcome!**
 
 MPRAsnakeflow pipeline processes sequencing data from Massively Parallel Reporter Assays (MPRAs)
 to create count tables for candidate sequences tested in the experiment.
 
-MPRAsnakeflow is built on top of `Snakemake <https://snakemake.readthedocs.io/>`_ (version 8 preferred) and is configured via a ``.yaml`` file.
+MPRAsnakeflow is built on top of `Snakemake <https://snakemake.readthedocs.io/>`_ (version ≥8.24.1 required) and is configured via a ``.yaml`` file.
 
 Authors
     Max Schubach (`@visze <https://github.com/visze>`_)
@@ -74,7 +74,7 @@ Features
    * - Option
      - Description
    * - ``--software-deployment-method``
-     - When ``conda`` is set, the utility uses mamba to efficiently query repositories and query package dependencies. MPRAsnakeflow also can use containers via apptainer by using ``--software-deployment-method apptainer``. Recommended option: ``--software-deployment-method conda apptainer``
+     - When ``conda`` is set, the utility uses conda to efficiently query repositories and query package dependencies. MPRAsnakeflow also can use containers via apptainer by using ``--software-deployment-method apptainer``. Recommended option: ``--software-deployment-method conda apptainer``
    * - ``--cores``
      - This utility sets the number of cores (``$N``) to be used by MPRAsnakeflow.
    * - ``--configfile``

docs/install.rst

@@ -19,7 +19,7 @@ Package management
 
 .. code-block:: bash
 
-    conda (mamba) 4.6 or above
+    conda >24.7.1 or above
 
 Download here: https://github.com/conda-forge/miniforge
 
@@ -36,7 +36,7 @@ Workflow language
 
 .. code-block:: bash
 
-    snakemake 8.16.0 or above (snakemake >=7.15.1 will also work but cli might be different as here documented)
+    snakemake 8.24.1 or above
 
 Download here: https://snakemake.readthedocs.io/
 
@@ -47,17 +47,17 @@ Clone repository
 Download here: https://github.com/kircherlab/MPRAsnakeflow.git
 
 
-Set up snakemake environment with conda/mamba
+Set up snakemake environment with conda
 =============================================
 
-This pipeline uses python2.7 and python3.6 with additional R scripts in a Snakemake pipeline. The ``.yml`` files provided will create the appropriate environments and is completely handled by MPRAsnakeflow. The whole pipeline is set up to run on a Linux system.
+This pipeline uses python2.7 and python ≥3.7 with additional R scripts in a Snakemake pipeline. The ``.yml`` files provided will create the appropriate environments and is completely handled by MPRAsnakeflow. The whole pipeline is set up to run on a Linux system.
 
 Install the the conda environment. The general conda environment is called ``snakemake``.
 
 .. code-block:: bash
 
     cd MPRAsnakeflow
-    mamba create -c conda-forge -c bioconda -n snakemake snakemake
+    conda create -c conda-forge -c bioconda -n snakemake snakemake
     
     # activate snakemake
     conda activate snakemake

workflow/Snakefile

@@ -23,7 +23,7 @@ import pandas as pd
 ##### check snakemake min version #####
 from snakemake.utils import min_version
 
-min_version("7.15.1")
+min_version("8.24.1")
 
 
 ##### report workflow #####