add the pairtools command to output final pairs file

modules/local/hicstuff/build_matrix.nf

@@ -11,6 +11,7 @@ process BUILD_MATRIX {
     output:
     tuple val(meta), path("${meta1.id}_*"), emit: matrix
     path "*.log", emit: log_file
+    path "*.gz", emit: final_pairs
 
     script:
 
@@ -21,6 +22,8 @@ process BUILD_MATRIX {
     grep -v ^# ${idx_pairs} | sort -S 2G -k8,8n -k9,9n --parallel=1 >> ${args}.pre.pairs
     hicstuff_build_matrix.py -p ${args}.pre.pairs -f ${fragments_list} -t graal -o ${args}
 
+    pairtools sort ${idx_pairs} --output ${idx_pairs}.gz --c1 chr1 --c2 chr2 --p1 pos1 --p2 pos2 --pt frag1
+
     mv ${args} ${meta1.id}_${args}
     mv hicstuff_matrix.log hicstuff_${meta1.id}_matrix_sparse.log
     """