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/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
@@ -14,6 +14,9 @@ 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/rules/asr.smk b/workflow/rules/asr.smk
@@ -4,22 +4,21 @@ rule reconstruct_ancestral_sequence:
     params:
         seed = 7291,
         seqtype = "DNA",
-        name = OUTPUT_NAME,
         outgroup = config["ALIGNMENT_REFERENCE"],
         model = config["TREE_MODEL"]
     input:
-        fasta = OUTDIR/"nextalign"/f"{OUTPUT_NAME}.aligned.masked.fasta"
+        fasta = "<results>/<dataset>/aligned.masked.fasta"
     output:
-        folder = directory(OUTDIR/"tree"),
-        state_file = OUTDIR/"tree"/f"{OUTPUT_NAME}.state"
+        folder = directory("<results>/<dataset>/tree"),
+        state_file = "<results>/<dataset>/tree/asr.state"
     log:
-        LOGDIR / "reconstruct_ancestral_sequence" / "log.txt"
+        "<logs>/<dataset>/reconstruct_ancestral_sequence/log.txt"
     shell:
         "mkdir -p {output.folder} && "
         "iqtree2 -seed {params.seed} "
-            "-asr "
-            "-o {params.outgroup} -T AUTO --threads-max {threads} -s {input.fasta} "
-            "--seqtype {params.seqtype} -m {params.model} --prefix {output.folder}/{params.name} >{log} 2>&1"
+        "-asr "
+        "-o {params.outgroup} -T AUTO --threads-max {threads} -s {input.fasta} "
+        "--seqtype {params.seqtype} -m {params.model} --prefix {output.folder}/asr >{log} 2>&1"
 
 
 rule ancestor_fasta:
@@ -30,10 +29,10 @@ rule ancestor_fasta:
         indeterminate_char = "N",
         name = "case_ancestor",
     input:
-        state_file = OUTDIR/"tree"/f"{OUTPUT_NAME}.state"
+        state_file = "<results>/<dataset>/tree/asr.state"
     output:
-        fasta = report(OUTDIR/f"{OUTPUT_NAME}.ancestor.fasta")
+        fasta = report("<results>/<dataset>/ancestor.fasta")
     log:
-        LOGDIR / "ancestor_fasta" / "log.txt"
+        "<logs>/<dataset>/ancestor_fasta/log.txt"
     script:
         "../scripts/ancestor_fasta.py"
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -49,7 +49,7 @@ def get_repo_version(base_dir: str, default: str, warn=False) -> str:
 def select_context_fasta():
     """Set context to be fetched automatically if CONTEXT_FASTA=null"""
     if "CONTEXT_FASTA" not in config.keys() or config["CONTEXT_FASTA"] is None:
-        return OUTDIR/"context"/"sequences.fasta"
+        return "<results>/<dataset>/context/sequences.fasta"
         if not Path(config["GISAID"]["CREDENTIALS"]).is_file():
             raise FileNotFoundError(f"Tried to download a context dataset, but no GISAID credentials were found at '{config['GISAID']['CREDENTIALS']}' (see README.md).")
     elif Path(config["CONTEXT_FASTA"]).is_file():
@@ -61,7 +61,7 @@ def select_context_fasta():
 def select_mapping_references_fasta():
     """Set mapping references to be fetched automatically if MAPPING_REFERENCES_FASTA=null"""
     if "MAPPING_REFERENCES_FASTA" not in config.keys() or config["MAPPING_REFERENCES_FASTA"] is None:
-        return OUTDIR/"mapping_references.fasta"
+        return "<results>/<dataset>/mapping_references.fasta"
     elif Path(config["MAPPING_REFERENCES_FASTA"]).is_file():
         return config["MAPPING_REFERENCES_FASTA"]
     else:
@@ -74,7 +74,7 @@ def is_url(string: str) -> bool:
 
 def select_problematic_vcf():
     if is_url(config["PROBLEMATIC_VCF"]):
-        return OUTDIR/"problematic_sites.vcf"
+        return "<results>/<dataset>/problematic_sites.vcf"
     elif Path(config["PROBLEMATIC_VCF"]).is_file():
         return config["PROBLEMATIC_VCF"]
     else: