edit multiqc_raw to force overwritting existing multiqc reports AND remove...

edit multiqc_raw to force overwritting existing multiqc reports AND remove line in fastqc_raw that created non-needed directory

rules/rawQC.smk

@@ -35,9 +35,6 @@ rule fastqc_raw:
     singularity: singularity_img
     shell:
         '''
-        # checks if output dir exist, created otherwise
-        [ ! -d {params.fastqc_dir}/{wildcards.dataset} ] && \
-        mkdir {params.fastqc_dir}/{wildcards.dataset}
         # Take a random sample of reads (1%) and process them with fastQC
         (reformat.sh in={input} out=stdout.fq samplerate={params.samplerate} | \
         fastqc -o {params.fastqc_dir}/{wildcards.dataset}_fastqc -f fastq \
@@ -72,5 +69,5 @@ rule multiqc_raw:
     singularity:singularity_img
     shell:
         '''
-        multiqc --file-list {input} --filename {output.multiqc_report}
+        multiqc -f --file-list {input} --filename {output.multiqc_report}
         '''