fix: remove option to define output dir in config.

rabioinf · rabioinf · commit 04542596282e · 2025-12-05T09:57:24.000+01:00
diff --git a/.test/config/config.yml b/.test/config/config.yml
@@ -1,5 +1,4 @@
 samplesheet: "config/samples.csv"
-outdir: "results"
 
 pgap:
   bin: "path/to/pgap.py"
diff --git a/config/config.yml b/config/config.yml
@@ -1,5 +1,4 @@
 samplesheet: "config/samples.csv"
-outdir: "results"
 
 pgap:
   bin: "path/to/pgap.py"
diff --git a/config/schemas/config.schema.yml b/config/schemas/config.schema.yml
@@ -6,9 +6,6 @@ properties:
   samplesheet:
     type: string
     description: Path to the sample sheet file
-  outdir:
-    type: string
-    description: Output directory for results
   pgap:
     type: object
     properties:
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -20,10 +20,7 @@ configfile: "config/config.yml"
 
 
 # set outout directory
-OUTDIR = config.get("outdir", "")
-
-if not OUTDIR:
-    OUTDIR = f"{os.getcwd()}/results"
+OUTDIR = f"{os.getcwd()}/results"
 
 
 # -----------------------------------------------------

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`samplesheet: "config/samples.csv"`
`2`		`-outdir: "results"`
`3`	`2`
`4`	`3`	`pgap:`
`5`	`4`	`bin: "path/to/pgap.py"`