diff --git a/README.md b/README.md index 2268cf7..cefb718 100644 --- a/README.md +++ b/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. @@ -33,9 +33,9 @@ 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). @@ -43,7 +43,7 @@ For installation details, see the [instructions in the Snakemake documentation]( 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: diff --git a/docs/cluster.rst b/docs/cluster.rst index 0b8028a..64c4288 100644 --- a/docs/cluster.rst +++ b/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 diff --git a/docs/contributing.rst b/docs/contributing.rst index bf81a5a..4f0c460 100644 --- a/docs/contributing.rst +++ b/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. diff --git a/docs/index.rst b/docs/index.rst index 3c5e3f4..eeece49 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -4,11 +4,11 @@ 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!** @@ -16,7 +16,7 @@ MPRAsnakeflow's documentation 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 `_ (version 8 preferred) and is configured via a ``.yaml`` file. +MPRAsnakeflow is built on top of `Snakemake `_ (version ≥8.24.1 required) and is configured via a ``.yaml`` file. Authors Max Schubach (`@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`` diff --git a/docs/install.rst b/docs/install.rst index df7dad5..79d2c29 100644 --- a/docs/install.rst +++ b/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 diff --git a/workflow/Snakefile b/workflow/Snakefile index 6abde68..b41e7eb 100644 --- a/workflow/Snakefile +++ b/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 #####