remove support of Snakemake v7

the minimum version for pathvars is 9.12

Author: ahmig

.github/workflows/install.yml

@@ -14,7 +14,7 @@ jobs:
         with:
           channel-priority: strict
           activate-environment: snakemake
-          environment-file: .test/environment_v7.yaml
+          environment-file: .test/environment_v9.yaml
       - name: Create environments
         shell: bash -el {0}
         run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml --conda-create-envs-only --use-conda -c1 --conda-frontend conda
@@ -29,7 +29,7 @@ jobs:
         with:
           channel-priority: strict
           activate-environment: snakemake
-          environment-file: .test/environment_v7.yaml
+          environment-file: .test/environment_v9.yaml
       - name: Dry run
         shell: bash -el {0}
         run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml --dry-run

.github/workflows/test_v7.yml

@@ -5,7 +5,7 @@ from snakemake.utils import min_version
 import subprocess
 
 
-min_version("7.19")
+min_version("9.12")
 
 # Workflow version
 __version__ = "test"

.test/Snakefile

@@ -10,7 +10,6 @@
 [![Zenodo DOI](https://zenodo.org/badge/627797162.svg)](https://doi.org/10.5281/zenodo.15771867)
 
 ![Install workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/install.yml/badge.svg)
-![Test workflow with Snakemake v7](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v7.yml/badge.svg)
 ![Test workflow with Snakemake v9](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v9.yml/badge.svg)
 ![Test workflow with Snakemake v9 and Apptainer](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_apptainer.yml/badge.svg)
 
@@ -24,7 +23,7 @@ configuring [the inputs and outputs](config/README.md#inputs-and-outputs) and
 [the context dataset](config/README.md#automated-construction-of-a-context-dataset):
 
 ```shell
-snakemake --use-conda --cores 4  # command for Snakemake v7
+snakemake --sdm conda --cores 4
 ```
 
 We provide a simple script that downloads the [data](https://doi.org/10.20350/digitalCSIC/15648) from [our study](https://doi.org/10.1093/ve/veae018)
@@ -40,8 +39,9 @@ It supports dependency management through either conda or Apptainer/Singularity,
 [run modes documentation](config/README.md#run-modes).
 
 We use continuous integration (CI) to automatically verify that all dependencies install correctly
-with Snakemake v7.32.4 (see GitHub Action `Install`), and to test that VIPERA runs
-successfully with Snakemake v7.32.4 and v9.15.0 using conda (Actions `Test Sm v(7|9)`).
+(see GitHub Action `Install`), and to test that VIPERA runs
+successfully using conda (Actions `Test Sm v(7|9)`).
+We run Snakemake v9.15.0 for these.
 We also test a containerized workflow with Snakemake v9.15.0 and Apptainer using a
 [remote image](https://hub.docker.com/r/ahmig/vipera) (Action `Test Sm v9 Apptainer`).
 This image is automatically updated in every version (Action `Deploy`).

.test/environment_v7.yaml

@@ -255,11 +255,10 @@ should be modified to fit your needs. Read more about Snakemake profiles
 [here](https://snakemake.readthedocs.io/en/stable/executing/cli.html#executing-profiles).
 To use the profile, install the
 [Snakemake executor plugin for SLURM](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html)
-and run one of the following commands:
+and run the following command:
 
 ```shell
-snakemake --slurm --profile profile/slurm  # Snakemake v7
-snakemake --profile profile/slurm          # Snakemake v8+
+snakemake --profile profile/slurm
 ```
 
 Additionally, we offer the option of running the workflow within a containerized