fix: switch to pathvars

pixi.toml

@@ -16,9 +16,9 @@ test = { features = ["test"] }
 format = { features = ["format"], no-default-feature = true }
 
 [feature.test.dependencies]
-pytest = "*"
-graphviz = "*"
+pytest = ">=9.0.2"
+graphviz = ">=12.2.1"
 
 [feature.format.dependencies]
-black = "*"
-snakefmt = "*"
+ruff = ">=0.15.1"
+snakefmt = ">=0.11.5"

workflow/Snakefile

@@ -38,6 +38,12 @@ snakemake.utils.validate(
 #####################
 ### Read Trimming ###
 #####################
+pathvars:
+    reports="reports",
+    stats="stats",
+    temp="temp",
+
+
 include: "rules/utils.smk"
 include: "rules/raw.smk"
 include: "rules/trim.smk"
@@ -79,34 +85,34 @@ rule multiqc:
         if is_activated("trim")
         else [],
     output:
-        html="reports/multiqc.html",
-        data="reports/multiqc_data.zip",
+        html="<reports>/multiqc.html",
+        data="<reports>/multiqc_data.zip",
     log:
-        "logs/reports/multiqc.log",
+        "<logs>/<reports>/multiqc.log",
     benchmark:
-        "benchmarks/reports/multiqc.jsonl"
-    params:
-        extra="--force --clean-up " + config.get("report", {}).get("multiqc", ""),
+        "<benchmarks>/<reports>/multiqc.jsonl"
     localrule: True
     threads: 1
     resources:
         mem=lambda w, attempt: f"{10* attempt} GiB",
         runtime=lambda w, attempt: f"{30* attempt} m",
+    params:
+        extra="--force --clean-up " + config.get("report", {}).get("multiqc", ""),
     wrapper:
         "v8.1.1/bio/multiqc"
 
 
 rule all:
+    default_target: True
     input:
         qc=rules.multiqc.output.html,
         res=(
             expand_pd(
-                "results/reads/trim/{sample}_{library}_{lane}_{read_type_trim}.fastq.gz",
+                "<results>/reads/trim/{sample}_{library}_{lane}_{read_type_trim}.fastq.gz",
                 units.explode("read_type_trim"),
             )
             if is_activated("trim")
             else []
         ),
     message:
         "Read trimming finished successfully!"
-    default_target: True

workflow/rules/raw.smk

@@ -44,7 +44,7 @@ rule get_fastq_raw:
     input:
         _get_input_data,
     output:
-        "results/reads/raw/{sample}_{library}_{lane}_{read_type_raw}.fastq.gz",
+        "<results>/reads/raw/{sample}_{library}_{lane}_{read_type_raw}.fastq.gz",
     localrule: True
     threads: 1
     run:
@@ -53,7 +53,9 @@ rule get_fastq_raw:
         src = Path(input[0])
         dst = Path(output[0])
         if src.suffix != ".gz":
-            raise ValueError("Input FASTQ files is not GZip'ed: {}!".format(input[0]))
+            raise ValueError(
+                "Input FASTQ files is not GZip'ed: {}!".format(input[0])
+            )
 
         with gzip.open(src, "rb") as f:
             f.read(2)
@@ -67,12 +69,12 @@ rule fastqc_raw:
     input:
         rules.get_fastq_raw.output,
     output:
-        html="stats/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}.html",
-        zip="stats/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}_fastqc.zip",
+        html="<stats>/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}.html",
+        zip="<stats>/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}_fastqc.zip",
     log:
-        "logs/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}.log",
+        "<logs>/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}.log",
     benchmark:
-        "benchmarks/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}.jsonl"
+        "<benchmarks>/reads/fastqc/raw/{sample}_{library}_{lane}_{read_type_raw}.jsonl"
     threads: 4
     resources:
         mem=lambda w, attempt: f"{3* attempt} GiB",