fix: need separate dirs for results because intermediate files do have non-unique names

Author: m-jahn

workflow/rules/common.smk

@@ -71,7 +71,9 @@ def get_final_input(wildcards):
         )
     if not config["rgi"]["skip"]:
         inputs += expand(
-            "results/qc/rgi/{sample}.{ext}", sample=samples.index, ext=["txt", "json"]
+            "results/qc/rgi/{sample}/result.{ext}",
+            sample=samples.index,
+            ext=["txt", "json"],
         )
     return inputs
 

workflow/rules/qc.smk

@@ -130,9 +130,9 @@ rule rgi_detection:
     input:
         fasta=rules.get_fasta.output.fasta,
     output:
-        multiext("results/qc/rgi/{sample}", ".txt", ".json"),
+        multiext("results/qc/rgi/{sample}/result", ".txt", ".json"),
     log:
-        "results/qc/rgi/{sample}.log",
+        "results/qc/rgi/{sample}/result.log",
     threads: max(workflow.cores * 0.25, 1)
     params:
         input_type="contig",