diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 96be2f378569298f184d6f6f1c8e7f559228f2c5..8155de603a54802996defe710fa64a2a56db07b3 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -433,19 +433,14 @@ rule fuse_bams:
 
 rule compute_coverage:
     input:
-        bam = rules.fuse_bams.output.sorted_bam,
+        sorted_bam = rules.fuse_bams.output.sorted_bam,
     output:
         coverage = OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{lib}_{rep}_on_C_elegans_coverage.txt"),
     params:
         genomelen = genomelen,
-    log:
-        coverage_log = OPJ(log_dir, "{trimmer}", "compute_coverage", "{lib}_{rep}.log"),
-        coverage_err = OPJ(log_dir, "{trimmer}", "compute_coverage", "{lib}_{rep}.err"),
     shell:
         """
-        # genomelen=$(samtools view -H {input} | grep "^@SQ" | awk -F ":" '{{sum+=$3}} END {{print sum}}')
-        # genomelen=$(samtools view -H {input} | grep -P '^@SQ' | cut -f 3 -d ':' | awk '{{sum+=$1}} END {{print sum}}')
-        bases=$(samtools depth {input} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
+        bases=$(samtools depth {input.sorted_bam} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
         python3 -c "print(${{bases}} / {params.genomelen})" > {output.coverage}
         """
 
@@ -540,17 +535,11 @@ rule htseq_count_reads:
         annot = biotype2annot,
     message:
         "Counting {wildcards.orientation} {wildcards.biotype} reads for {wildcards.lib}_{wildcards.rep} with htseq-count."
+    benchmark:
+        OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}_benchmark.txt")
     log:
-        log = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}.log"),
-        err = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}.err")
-    #shell:
-    #    """
-    #    annot="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/{wildcards.biotype}.gtf"
-    #    converter="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes_id2name.pickle"
-    #    cmd="htseq-count -f bam -s {params.stranded} -a 0 -t transcript -i gene_id {input.sorted_bam} ${{annot}} | tee {output.counts} | id2name.py ${{converter}} > {output.counts_converted}"
-    #    echo ${{cmd}}
-    #    eval ${{cmd}} > {log}
-    #    """
+        log = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.log"),
+        err = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err")
     wrapper:
         "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/htseq_count_reads"
 
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 4fb828b0cebb432aebbb78bff43750e9cf434139..2321af30200539013f2c005ac7d0e0261b850f91 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -803,18 +803,14 @@ rule sam2indexedbam:
 
 rule compute_coverage:
     input:
-        rules.sam2indexedbam.output.sorted_bam,
+        sorted_bam = rules.sam2indexedbam.output.sorted_bam,
     output:
         coverage = OPJ(output_dir, aligner, "mapped_C_elegans", "{lib}_{rep}", "{read_type}_on_C_elegans_coverage.txt"),
     params:
         genomelen = genomelen,
-    # Currently not used
-    #log:
-    #    log = OPJ(log_dir, "compute_coverage", "{lib}_{rep}_{read_type}.log"),
-    #    err = OPJ(log_dir, "compute_coverage", "{lib}_{rep}_{read_type}.err"),
     shell:
         """
-        bases=$(samtools depth {input} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
+        bases=$(samtools depth {input.sorted_bam} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
         python3 -c "print(${{bases}} / {params.genomelen})" > {output.coverage}
         """