diff --git a/bam2bigwig.sh b/bam2bigwig.sh
index 39b7a202a349dd1cd906a268c03405d4a5b0ef96..d71be2ce3116ed820d8ff225d8614029659ec543 100755
--- a/bam2bigwig.sh
+++ b/bam2bigwig.sh
@@ -126,16 +126,17 @@ samtools view -H ${bam} \
 
 compute_coverage()
 {
-    cmd="niceload --noswap -q bedtools genomecov -bg -split ${orient_filter} ${scaling} -ibam ${bam}"
+    cmd="niceload --noswap bedtools genomecov -bg -split ${orient_filter} ${scaling} -ibam ${bam}"
     eval ${cmd} \
         | mawk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \
         || error_exit "compute_coverage failed"
         #|| cleanup && error_exit "compute_coverage failed"
 }
 
+# TODO: find how to run this with niceload (there may be an issue with the quoting)
 make_bins()
 {
-    cmd="niceload --noswap -q bedmap --faster --echo --mean --delim \"\t\" --skip-unmapped ${bin_file} -"
+    cmd="bedmap --faster --echo --mean --delim \"\t\" --skip-unmapped ${bin_file} -"
     eval ${cmd} || error_exit "make_bins failed"
     #eval ${cmd} || cleanup && error_exit "make_bins failed"
 }
@@ -145,7 +146,7 @@ compute_coverage | make_bins \
     #> ${bedgraph} || cleanup && error_exit "generating bedgraph failed"
 
 echo "making bigwig"
-niceload --noswap -q bedGraphToBigWig ${bedgraph} ${genome_file} ${bigwig} || error_exit "bedGraphToBigWig failed"
+niceload --noswap bedGraphToBigWig ${bedgraph} ${genome_file} ${bigwig} || error_exit "bedGraphToBigWig failed"
 #bedGraphToBigWig ${bedgraph} ${genome_file} ${bigwig} || cleanup && error_exit "bedGraphToBigWig failed"
 
 echo "removing ${bedgraph}"
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index a01e4d724f31fbe36b46ae403375def85f3dd5e9..1708687a37ebf76a3521787c86f2fc4beae5b78a 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -1159,7 +1159,7 @@ rule feature_count_reads:
     shell:
         """
         tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "feature_{wildcards.lib}_{wildcards.rep}_{wildcards.read_type}_{wildcards.mapping_type}_{wildcards.biotype}_{wildcards.orientation}_{wildcards.feature_type}.XXXXXXXXXX")
-        cmd="niceload --noswap -q featureCounts {params.min_mapq} -a {params.annot} -o {output.counts} -t {wildcards.feature_type} -g "gene_id" -O -s {params.stranded} --fracOverlap 1 --tmpDir ${{tmpdir}} {input}"
+        cmd="niceload --noswap featureCounts {params.min_mapq} -a {params.annot} -o {output.counts} -t {wildcards.feature_type} -g "gene_id" -O -s {params.stranded} --fracOverlap 1 --tmpDir ${{tmpdir}} {input}"
         featureCounts -v 2> {log.log}
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
@@ -1458,7 +1458,7 @@ rule small_RNA_seq_annotate:
         mem_mb=19150
     shell:
         """
-        niceload --noswap -q small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -g {input.merged_gtf} \\
+        niceload --noswap small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -g {input.merged_gtf} \\
             -r {params.reads_out_dir} -o {params.counts_out_dir} -l {log.mapped_log}
         """
 
@@ -1509,7 +1509,7 @@ rule small_RNA_seq_annotate_U:
         mem_mb=14700
     shell:
         """
-        niceload --noswap -q small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -u -g {input.merged_gtf} \\
+        niceload --noswap small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -u -g {input.merged_gtf} \\
             -r {params.reads_out_dir} -o {params.counts_out_dir} -l {log.mapped_log}
         """
 
@@ -2657,7 +2657,7 @@ your deepTools settings and check your input files.
 #"""
         try:
             shell("""
-                cmd="niceload --noswap -q bamCoverage -b {input.bam} --skipNAs {params.orient_filter} \\
+                cmd="niceload --noswap bamCoverage -b {input.bam} --skipNAs {params.orient_filter} \\
                     -of=bigwig -bs 10 -p={threads} \\
                     -o {output.bigwig} \\
                     1>> {log.log} 2>> {log.err}"
@@ -2722,7 +2722,7 @@ bam2bigwig.sh: bedGraphToBigWig failed
 """
             try:
                 shell("""
-                    niceload --noswap -q bam2bigwig.sh {input.bam} {params.genome_binned} \\
+                    niceload --noswap bam2bigwig.sh {input.bam} {params.genome_binned} \\
                         {wildcards.lib}_{wildcards.rep} {wildcards.orientation} F \\
                         %f {output.bigwig_norm} \\
                         > {log.log} 2> {log.err} \\
@@ -3417,22 +3417,25 @@ rule plot_biotype_mean_meta_profile:
     shell:
         """
         tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "plot_meta_profile_meta_scale_{wildcards.meta_scale}_{wildcards.read_type}_by_{wildcards.norm}_{wildcards.orientation}_{wildcards.type_set}_{wildcards.biotype}_{wildcards.min_len}_{wildcards.group_type}_{wildcards.lib_group}.XXXXXXXXXX")
-        niceload --noswap -q computeMatrix scale-regions -S {input.bws} \\
+        echo "tmpdir=\\"${{tmpdir}}\\"" 1> {log.log}
+        cmd="computeMatrix scale-regions -S {input.bws} \\
             -R {input.bed} \\
             {params.meta_params} \\
             -p {threads} \\
-            -out ${{tmpdir}}/meta_profile.gz \\
-            1> {log.log} \\
+            -out ${{tmpdir}}/meta_profile.gz"
+        echo "${{cmd}}" 1>> {log.log}
+        niceload --noswap ${{cmd}} \\
+            1>> {log.log} \\
             2> {log.err} \\
             || error_exit "computeMatrix failed"
         cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\
             -z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.biotype} \\
-            -y \\'{params.y_label}\\' \\
+            -y \\"{params.y_label}\\" \\
             --samplesLabel {params.labels} \\
             --perGroup \\
             --labelRotation 90"
-        echo ${{cmd}} 1>> {log.log} \\
-        niceload --noswap -q eval ${{cmd}} \\
+        echo "${{cmd}}" 1>> {log.log}
+        niceload --noswap ${{cmd}} \\
             1>> {log.log} \\
             2>> {log.err} \\
             || error_exit "plotProfile failed"
@@ -3467,21 +3470,24 @@ rule plot_gene_list_mean_meta_profile:
     shell:
         """
         tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "plot_meta_profile_meta_scale_{wildcards.meta_scale}_{wildcards.read_type}_by_{wildcards.norm}_{wildcards.orientation}_{wildcards.type_set}_{wildcards.id_list}_{wildcards.group_type}_{wildcards.lib_group}.XXXXXXXXXX")
-        niceload --noswap -q computeMatrix scale-regions -S {input.bws} \\
+        echo "tmpdir=\\"${{tmpdir}}\\"" 1> {log.log}
+        cmd="computeMatrix scale-regions -S {input.bws} \\
             -R {input.bed} \\
             {params.meta_params} \\
             -p 1 \\
-            -out ${{tmpdir}}/meta_profile.gz \\
-            1> {log.log} \\
+            -out ${{tmpdir}}/meta_profile.gz"
+        echo "${{cmd}}" 1>> {log.log}
+        niceload --noswap ${{cmd}} \\
+            1>> {log.log} \\
             2> {log.err} \\
             || error_exit "computeMatrix failed"
         cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\
             -z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.id_list} \\
-            -y \\'{params.y_label}\\' \\
+            -y \\"{params.y_label}\\" \\
             --samplesLabel {params.labels} \\
             --perGroup"
-        echo ${{cmd}} 1>> {log.log}
-        niceload --noswap -q eval ${{cmd}} \\
+        echo "${{cmd}}" 1>> {log.log}
+        niceload --noswap ${{cmd}} \\
             1>> {log.log} \\
             2>> {log.err} \\
             || error_exit "plotProfile failed"
@@ -3578,8 +3584,9 @@ rule plot_pi_targets_profile:
                 # We should compute -bs, -b, and -a from PI_MIN
                 shell("""
 tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "plot_pi_targets_profile_{wildcards.lib}_{wildcards.rep}_{wildcards.read_type}_by_{wildcards.norm}_{wildcards.orientation}_{wildcards.biotype}.XXXXXXXXXX")
+echo "tmpdir=\\"${{tmpdir}}\\"" 1> {log.log}
 # 501 and 21 are multiples of 3
-niceload --noswap -q computeMatrix scale-regions -S {input.bigwig} \\
+niceload --noswap computeMatrix scale-regions -S {input.bigwig} \\
     -R {input.bed} \\
     -bs 3 \\
     -b 1002 \\
@@ -3587,15 +3594,15 @@ niceload --noswap -q computeMatrix scale-regions -S {input.bigwig} \\
     -a 1002 \\
     -p {threads} \\
     -out ${{tmpdir}}/meta_profile.gz \\
-    1> {log.log} \\
+    1>> {log.log} \\
     2> {log.err} \\
     || error_exit "computeMatrix failed"
 cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output.figure} \\
-    -y \\'{params.y_label}\\' \\
-    --startLabel \\'\\' \\
-    --endLabel \\'\\'"
-echo ${{cmd}} 1>> {log.log}
-niceload --noswap -q eval ${{cmd}} \\
+    -y \\"{params.y_label}\\" \\
+    --startLabel \\"\\" \\
+    --endLabel \\"\\""
+echo "${{cmd}}" 1>> {log.log}
+niceload --noswap ${{cmd}} \\
     1>> {log.log} \\
     2>> {log.err} \\
     || error_exit "plotProfile failed"