fix cpu usage from hicstuff functions

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)

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