diff --git a/workflow/rules/qc-fastq.smk b/workflow/rules/qc-fastq.smk index 7178fb8..d8dca73 100644 --- 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 index 8cb5435..dc0be5c 100644 --- 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):