Add warning about invalid setting combination for trimming

moiexpositoalonsolab · Oct 11, 2024 · 4fc3386 · 4fc3386
1 parent d961775
commit 4fc3386
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/workflow/rules/qc-fastq.smk b/workflow/rules/qc-fastq.smk
@@ -50,7 +50,12 @@ elif config["params"]["fastqc"]["input"] == "trimmed":
         trimmed = get_trimmed_reads(wc)
 
         # Now let's see if we have merged them or not, and add to our result accordingly.
-        if config["settings"]["merge-paired-end-reads"]:
+        if config["settings"]["trimming-tool"] == "none":
+            raise Exception(
+                "Invalid setting for fastqc: Selected 'settings: trimming-tool: \"none\"' "
+                + "in combination with 'params: fastqc: input: \"trimmed\"'."
+            )
+        elif config["settings"]["merge-paired-end-reads"]:
             assert len(trimmed) == 1
             add_fastqc_file(smp.sample, smp.unit, "trimmed-merged", trimmed[0])
         else:

diff --git a/workflow/rules/trimming-none.smk b/workflow/rules/trimming-none.smk
@@ -5,7 +5,7 @@
 
 def get_trimmed_reads(wildcards):
     # Simply forward the files to their original fastq files.
-    return get_fastq(wildcards).values()
+    return list(get_fastq(wildcards).values())
 
 
 def get_trimming_report(sample, unit):