correct bug counts

Snakefile

@@ -240,6 +240,7 @@ if config["feature_counts"]["do"]:
     feature_counts_gff  = config['genome']['gff_file']
     feature_counts_logs_err = "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.err"
     feature_counts_logs_out = "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.out"
+    feature_counts_options = config['feature_counts']['options']
     final_output.extend(expand(feature_counts_output_count, SAMPLE=samples, REF=ref, MAP=mapper))
     include: os.path.join(RULES, "feature_counts.rules")
 

workflow/rules/feature_counts.rules

@@ -28,7 +28,7 @@ rule feature_counts:
         bam = feature_counts_input,
         gff = feature_counts_gff
     output:
-        count = feature_counts_output_count
+        feature_counts_output_count
 
     singularity:
         "rnaflow.img"
@@ -43,7 +43,7 @@ rule feature_counts:
         "subread/1.6.1"
     shell:
         """
-        featureCounts -T {threads} {params.mapp} -a {input.gff} -o {output.count} {input.bam} {params.input} 2> {log}
+        featureCounts -T {threads} {params.mapp} -a {input.gff} -o {output} {input.bam} {params.input} 2> {log}
         """