diff --git a/modules/local/hicstuff/cutsite.nf b/modules/local/hicstuff/cutsite.nf
index acba59ab566b83473a7b85bceee43f4d5d1ada2a..161eed1a8e7039ed2e416f5d80277125a6feefb9 100644
--- a/modules/local/hicstuff/cutsite.nf
+++ b/modules/local/hicstuff/cutsite.nf
@@ -19,7 +19,7 @@ process CUTSITE {
     def output_rev = task.ext.output_rev ?: "${meta2.id}_${meta2.chunk}_${meta2.mates}.fastq"
 
     """
-    hicstuff_cutsite.py -r1 ${reads1} -r2 ${reads2} -e ${digestion} -o1 ${output_for} -o2 ${output_rev} ${args}
+    hicstuff_cutsite.py -r1 ${reads1} -r2 ${reads2} -e ${digestion} -o1 ${output_for} -o2 ${output_rev} -c ${task.cpus} ${args}
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         hicstuff: v3.1.3)
diff --git a/modules/local/hicstuff/iteralign.nf b/modules/local/hicstuff/iteralign.nf
index 82ad24a4eccc2f306c734147d019b3c9f9fe0339..d455a7c1bc940dd0ba20be384e9e54c93a0d45c4 100644
--- a/modules/local/hicstuff/iteralign.nf
+++ b/modules/local/hicstuff/iteralign.nf
@@ -22,7 +22,7 @@ process ITERALIGN {
     [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
     [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
 
-    hicstuff_iteralign.py -r ${reads} -g \$INDEX -b ${prefix}.bam ${args}
+    hicstuff_iteralign.py -r ${reads} -g \$INDEX -b ${prefix}.bam -n ${task.cpus} ${args}
 
     samtools view -F 2048 -h -@ $task.cpus -O BAM ${prefix}.bam -o ${prefix}_iteraligned.bam