minor

Snakefile.smk

@@ -25,7 +25,7 @@ rule final_outs:
     input:
         "{outdir}/multiqc/multiqc_report_fastqc.html".format(outdir=config["outdir"]),
         "{outdir}/multiqc/multiqc_report_bam.html".format(outdir=config["outdir"]),
-        "{outdir}/gene_count_dicoexpress.csv".format(outdir=config["outdir"])
+        expand("{outdir}/variant/{sample}_freebayes.vcf", outdir=config["outdir"], sample=samples['SampleName'])
 
 #function return only the fastq1 file and adds the fastq path
 def get_fastq1(wildcards):