PathoGenOmics-Lab · ahmig · May 3, 2026 · May 3, 2026 · May 3, 2026 · May 3, 2026
diff --git a/.github/workflows/install.yml b/.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
diff --git a/.github/workflows/test_apptainer.yml b/.github/workflows/test_apptainer.yml
@@ -30,8 +30,8 @@ jobs:
       - name: Pack logs
         if: success() || failure()
         shell: bash -el {0}
-        run: tar czf logs.tar.gz .test/output .snakemake/log
-      - name: Upload output file
+        run: tar czf logs.tar.gz logs .snakemake/log
+      - name: Upload logs file
         if: success() || failure()
         uses: actions/upload-artifact@v4
         with:

diff --git a/.github/workflows/test_v7.yml b/.github/workflows/test_v7.yml
diff --git a/.github/workflows/test_v9.yml b/.github/workflows/test_v9.yml
@@ -30,8 +30,8 @@ jobs:
       - name: Pack logs
         if: success() || failure()
         shell: bash -el {0}
-        run: tar czf logs.tar.gz .test/output .snakemake/log
-      - name: Upload output file
+        run: tar czf logs.tar.gz logs .snakemake/log
+      - name: Upload logs file
         if: success() || failure()
         uses: actions/upload-artifact@v4
         with:

diff --git a/.gitignore b/.gitignore
@@ -3,7 +3,8 @@
 
 # Analysis files
 /data/
-/output/
+/results/
+/logs/
 
 # MAC
 .DS_Store

diff --git a/.test/Snakefile b/.test/Snakefile
@@ -5,11 +5,14 @@ from snakemake.utils import min_version
 import subprocess
 
 
-min_version("7.19")
+min_version("9.12")
 
 # Workflow version
 __version__ = "test"
 
+pathvars:
+    dataset = config["OUTPUT_NAME"]
+
 # Rules
 include: "../workflow/core.smk"
 include: "../workflow/rules/demix.smk"
@@ -19,4 +22,4 @@ include: "../workflow/rules/report.smk"
 
 rule all:
     input:
-        OUTDIR/f"{OUTPUT_NAME}.report.html"
+        "<results>/<dataset>/report.html"
diff --git a/.test/environment_v7.yaml b/.test/environment_v7.yaml
diff --git a/.test/targets.yaml b/.test/targets.yaml
@@ -10,8 +10,6 @@ SAMPLES:
     fasta: ".test/data/fasta/sample3.fasta"
 METADATA:
   ".test/data/metadata.csv"
-OUTPUT_DIRECTORY:
-  ".test/output"
 CONTEXT_FASTA:
   ".test/data/context.fasta"
 OUTPUT_NAME:

diff --git a/Dockerfile b/Dockerfile
@@ -1,9 +1,6 @@
 FROM condaforge/miniforge3:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="fb2a04b98efa75d8b830a16722a8717eb91a3c66659e3c78b90b0cee3a50db69"
-
-# Step 2: Retrieve conda environments
-
+LABEL io.github.snakemake.conda_env_hash="405c5473ec0f18eae88ec6de97e8b3689fe0fb53cced156e8f6efe589c815a36"
 # Conda environment:
 #   source: workflow/envs/afwdist.yaml
 #   prefix: /conda-envs/9c24a867826615972cc288081976e7fc
@@ -14,20 +11,19 @@ LABEL io.github.snakemake.conda_env_hash="fb2a04b98efa75d8b830a16722a8717eb91a3c
 #     - afwdist==1.0.0
 RUN mkdir -p /conda-envs/9c24a867826615972cc288081976e7fc
 COPY workflow/envs/afwdist.yaml /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/biopython.yaml
-#   prefix: /conda-envs/162796cecea22d99c8702138f0c48e2f
+#   prefix: /conda-envs/0744a49115d0593f017b8400a3000df0
 #   channels:
 #     - conda-forge
 #     - bioconda
+#     - nodefaults
 #   dependencies:
-#     - python==3.10
-#     - biopython==1.81
-#     - pandas==2.0.3
-RUN mkdir -p /conda-envs/162796cecea22d99c8702138f0c48e2f
-COPY workflow/envs/biopython.yaml /conda-envs/162796cecea22d99c8702138f0c48e2f/environment.yaml
-
+#     - python==3.14.6
+#     - biopython==1.87
+#     - pandas==3.0.3
+RUN mkdir -p /conda-envs/0744a49115d0593f017b8400a3000df0
+COPY workflow/envs/biopython.yaml /conda-envs/0744a49115d0593f017b8400a3000df0/environment.yaml
 # Conda environment:
 #   source: workflow/envs/fetch.yaml
 #   prefix: /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a
@@ -39,7 +35,6 @@ COPY workflow/envs/biopython.yaml /conda-envs/162796cecea22d99c8702138f0c48e2f/e
 #     - curl
 RUN mkdir -p /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a
 COPY workflow/envs/fetch.yaml /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/freyja.yaml
 #   prefix: /conda-envs/bb4c5f3a509433cc08861582fab4a705
@@ -50,7 +45,6 @@ COPY workflow/envs/fetch.yaml /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a/envir
 #     - freyja==2.0.1
 RUN mkdir -p /conda-envs/bb4c5f3a509433cc08861582fab4a705
 COPY workflow/envs/freyja.yaml /conda-envs/bb4c5f3a509433cc08861582fab4a705/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/gisaidr.yaml
 #   prefix: /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f
@@ -64,7 +58,6 @@ COPY workflow/envs/freyja.yaml /conda-envs/bb4c5f3a509433cc08861582fab4a705/envi
 RUN mkdir -p /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f
 COPY workflow/envs/gisaidr.yaml /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f/environment.yaml
 COPY workflow/envs/gisaidr.post-deploy.sh /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f/post-deploy.sh
-
 # Conda environment:
 #   source: workflow/envs/iqtree.yaml
 #   prefix: /conda-envs/0a608afb24723cb6fa8aef748f5efbc8
@@ -75,7 +68,6 @@ COPY workflow/envs/gisaidr.post-deploy.sh /conda-envs/3fad3c9cdfa40bee9404f6a2e8
 #     - iqtree==2.2.2.3
 RUN mkdir -p /conda-envs/0a608afb24723cb6fa8aef748f5efbc8
 COPY workflow/envs/iqtree.yaml /conda-envs/0a608afb24723cb6fa8aef748f5efbc8/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/nextalign.yaml
 #   prefix: /conda-envs/04a3347f94ddf7e21c34bc49e5246076
@@ -86,7 +78,6 @@ COPY workflow/envs/iqtree.yaml /conda-envs/0a608afb24723cb6fa8aef748f5efbc8/envi
 #     - nextalign==2.13
 RUN mkdir -p /conda-envs/04a3347f94ddf7e21c34bc49e5246076
 COPY workflow/envs/nextalign.yaml /conda-envs/04a3347f94ddf7e21c34bc49e5246076/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/pangolin.yaml
 #   prefix: /conda-envs/fb978640cd765c8a63bbcdc01f3a206b
@@ -99,7 +90,6 @@ COPY workflow/envs/nextalign.yaml /conda-envs/04a3347f94ddf7e21c34bc49e5246076/e
 #     - setuptools<81
 RUN mkdir -p /conda-envs/fb978640cd765c8a63bbcdc01f3a206b
 COPY workflow/envs/pangolin.yaml /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/quarto_render.yaml
 #   prefix: /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1
@@ -114,7 +104,6 @@ COPY workflow/envs/pangolin.yaml /conda-envs/fb978640cd765c8a63bbcdc01f3a206b/en
 #     - r-heatmaply==1.6.0
 RUN mkdir -p /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1
 COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9c1/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/renv.yaml
 #   prefix: /conda-envs/fe892aca096e6b2883923c8755f9ac77
@@ -136,7 +125,6 @@ COPY workflow/envs/quarto_render.yaml /conda-envs/96f3c1cec4b3ce5d72f708992272e9
 #     - r-logger==0.2.2
 RUN mkdir -p /conda-envs/fe892aca096e6b2883923c8755f9ac77
 COPY workflow/envs/renv.yaml /conda-envs/fe892aca096e6b2883923c8755f9ac77/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/snpeff.yaml
 #   prefix: /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95
@@ -147,7 +135,6 @@ COPY workflow/envs/renv.yaml /conda-envs/fe892aca096e6b2883923c8755f9ac77/enviro
 #     - snpsift==5.1d
 RUN mkdir -p /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95
 COPY workflow/envs/snpeff.yaml /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/tools.yaml
 #   prefix: /conda-envs/1f283441022c3c9d97669994a3c5e8bb
@@ -159,7 +146,6 @@ COPY workflow/envs/snpeff.yaml /conda-envs/0adafb79cb1bec58ef4c77bf4cca4f95/envi
 #     - bcftools==1.23
 RUN mkdir -p /conda-envs/1f283441022c3c9d97669994a3c5e8bb
 COPY workflow/envs/tools.yaml /conda-envs/1f283441022c3c9d97669994a3c5e8bb/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/var_calling.yaml
 #   prefix: /conda-envs/81e46c677a6cc0618c93963d57d17d3f
@@ -173,10 +159,8 @@ COPY workflow/envs/tools.yaml /conda-envs/1f283441022c3c9d97669994a3c5e8bb/envir
 RUN mkdir -p /conda-envs/81e46c677a6cc0618c93963d57d17d3f
 COPY workflow/envs/var_calling.yaml /conda-envs/81e46c677a6cc0618c93963d57d17d3f/environment.yaml
 
-# Step 3: Generate conda environments
-
 RUN conda env create --prefix /conda-envs/9c24a867826615972cc288081976e7fc --file /conda-envs/9c24a867826615972cc288081976e7fc/environment.yaml && \
-    conda env create --prefix /conda-envs/162796cecea22d99c8702138f0c48e2f --file /conda-envs/162796cecea22d99c8702138f0c48e2f/environment.yaml && \
+    conda env create --prefix /conda-envs/0744a49115d0593f017b8400a3000df0 --file /conda-envs/0744a49115d0593f017b8400a3000df0/environment.yaml && \
     conda env create --prefix /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a --file /conda-envs/9439457f932a4fbca3665c9ea1ac2f0a/environment.yaml && \
     conda env create --prefix /conda-envs/bb4c5f3a509433cc08861582fab4a705 --file /conda-envs/bb4c5f3a509433cc08861582fab4a705/environment.yaml && \
     conda env create --prefix /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f --file /conda-envs/3fad3c9cdfa40bee9404f6a2e8fda69f/environment.yaml && \

diff --git a/README.md b/README.md
@@ -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`).

diff --git a/build_targets.py b/build_targets.py
@@ -91,7 +91,6 @@ def find_file_with_extension(directory: Path, prefix: str, extensions: List[str]
     else:
         sys.exit(f"ERROR: metadata file '{args.metadata_csv}' does not exist")
     targets["OUTPUT_NAME"] = args.output_name
-    targets["OUTPUT_DIRECTORY"] = "output"
     targets["CONTEXT_FASTA"] = None
     targets["MAPPING_REFERENCES_FASTA"] = None
 

diff --git a/config/README.md b/config/README.md
@@ -37,8 +37,7 @@ The path to these input files is set in two configuration files in YAML format:
 [config.yaml](/config/config.yaml) (for general workflow settings) and
 [targets.yaml](/config/targets.yaml) (for specific dataset-related settings).
 The latter must be modified by the user to point the `SAMPLES` and `METADATA`
-parameters to your data. The `OUTPUT_DIRECTORY` parameter should point to your
-desired results directory.
+parameters to your data.
 
 The script [`build_targets.py`](/build_targets.py) simplifies the process of creating
 the targets configuration file. To run this script, you need to have PyYAML installed. It
@@ -62,8 +61,6 @@ SAMPLES:
   ...
 METADATA:
   "path/to/metadata.csv"
-OUTPUT_DIRECTORY:
-  "output"
 CONTEXT_FASTA:
   null
 MAPPING_REFERENCES_FASTA:
@@ -258,11 +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

diff --git a/config/targets.yaml b/config/targets.yaml
@@ -39,8 +39,6 @@ METADATA:
   "data/metadata.csv"
 OUTPUT_NAME:
   "case_study"
-OUTPUT_DIRECTORY:
-  "output"
 CONTEXT_FASTA:
   null
 MAPPING_REFERENCES_FASTA:

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -7,13 +7,16 @@ import subprocess
 min_version("7.19")
 
 with open(Path(workflow.basedir).parent / "version.txt") as f:
-    __version__ = f.read()
+    __version__ = f.read().strip()
 
 containerized: "docker://ahmig/vipera:v" + __version__
 
 configfile: "config/config.yaml"
 configfile: "config/targets.yaml"
 
+pathvars:
+    dataset = config["OUTPUT_NAME"]
+
 include: "core.smk"
 include: "rules/context.smk"
 include: "rules/demix.smk"
@@ -22,4 +25,4 @@ include: "rules/report.smk"
 
 rule all:
     input:
-        OUTDIR/f"{OUTPUT_NAME}.report.html"
+        "<results>/<dataset>/report.html"
diff --git a/workflow/core.smk b/workflow/core.smk
@@ -1,18 +1,5 @@
-BASE_PATH = Path(workflow.basedir).parent.resolve()
-
 include: "rules/common.smk"
 
-# Outputs
-OUTPUT_NAME = config["OUTPUT_NAME"]
-OUTDIR = Path(config["OUTPUT_DIRECTORY"])
-
-# Logging
-LOGDIR = OUTDIR / "logs"
-
-# Report
-REPORT_DIR_PLOTS = Path(OUTDIR/"report/plots")
-REPORT_DIR_TABLES = Path(OUTDIR/"report/tables")
-
 include: "rules/fetch.smk"
 include: "rules/fasta.smk"
 include: "rules/asr.smk"

diff --git a/workflow/envs/biopython.yaml b/workflow/envs/biopython.yaml
@@ -1,7 +1,8 @@
 channels:
   - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
-  - python==3.10
-  - biopython==1.81
-  - pandas==2.0.3
+  - python==3.14.6
+  - biopython==1.87
+  - pandas==3.0.3