diff --git a/snakePipes/shared/rules/DESeq2.singleComp.snakefile b/snakePipes/shared/rules/DESeq2.singleComp.snakefile
index 538a0fa85..ae00b05fd 100644
--- a/snakePipes/shared/rules/DESeq2.singleComp.snakefile
+++ b/snakePipes/shared/rules/DESeq2.singleComp.snakefile
@@ -19,27 +19,29 @@ rule DESeq2:
         outdir = get_outdir("DESeq2",sampleSheet),
         fdr = fdr,
         importfunc = os.path.join(maindir, "shared", "rscripts", "DE_functions.R"),
-        allele_info = lambda wildcards : 'TRUE' if 'allelic-mapping' in mode else 'FALSE',
+        allele_info = lambda wildcards : 'TRUE' if 'allelic-mapping' in mode or "allelic-counting" in mode else 'FALSE',
         tx2gene_file = 'NA',
         rmdTemplate = os.path.join(maindir, "shared", "rscripts", "DESeq2Report.Rmd"),
-        formula = config["formula"]
+        formula = config["formula"],
+        counts_table = lambda wildcards,input: os.path.join(outdir,input.counts_table)
     log:
         out = "{}/logs/DESeq2.out".format(get_outdir("DESeq2",sampleSheet)),
         err = "{}/logs/DESeq2.err".format(get_outdir("DESeq2",sampleSheet))
     conda: CONDA_RNASEQ_ENV
-    shell:
-        "cd {params.outdir} && "
-        "Rscript {params.script} "
-        "{input.sampleSheet} " # 1
-        "../{input.counts_table} " # 2
-        "{params.fdr} " # 3
-        "../{input.symbol_file} " # 4
-        "{params.importfunc} " # 5
-        "{params.allele_info} " # 6
-        "{params.tx2gene_file} " # 7
-        "{params.rmdTemplate} " # 8
-        "{params.formula} " #9
-        " > ../{log.out} 2> ../{log.err}"
+    script: "{params.script}"
+#    shell:
+#        "cd {params.outdir} && "
+#        "Rscript {params.script} "
+#        "{input.sampleSheet} " # 1
+#        "../{input.counts_table} " # 2
+#        "{params.fdr} " # 3
+#        "../{input.symbol_file} " # 4
+#        "{params.importfunc} " # 5
+#        "{params.allele_info} " # 6
+#        "{params.tx2gene_file} " # 7
+#        "{params.rmdTemplate} " # 8
+#        "{params.formula} " #9
+#        " > ../{log.out} 2> ../{log.err}"
 
 
 ## DESeq2 (on Salmon)