remove bash integer convertion

src/modules/sample_reads.nf

@@ -120,15 +120,15 @@ process SAMPLE_READS {
         error "SEQTK/SAMPLE must have a sample_size value included"
     }
     """
-    SAMPLE_SIZE=\$((cat $sample_size | tr -d '\\n'))
-    CURRENT_READ_NUMBER=\$((cat $read_number | tr -d '\\n'))
+    SAMPLE_SIZE=\$(cat $sample_size | tr -d '\\n')
+    CURRENT_READ_NUMBER=\$(cat $read_number | tr -d '\\n')
 
     if [\$SAMPLE_SIZE -eq \$CURRENT_READ_NUMBER]; then
         ln -s ${reads} sample_${reads}
-        READ_NUMBER=\$((cat $sample_size | tr -d '\\n'))
+        READ_NUMBER=\$(cat $sample_size | tr -d '\\n')
     else
-        zcat ${reads} | head -n \$((cat $sample_size | tr -d '\\n')) | gzip -c > sample_${reads}
-        READ_NUMBER=\$((zcat sample_${reads} | wc -l))
+        zcat ${reads} | head -n \$(cat $sample_size | tr -d '\\n') | gzip -c > sample_${reads}
+        READ_NUMBER=\$(zcat sample_${reads} | wc -l)
     fi
     if [\$SAMPLE_SIZE -ne \$READ_NUMBER]; then
        exit 1 

src/modules/split.nf

@@ -17,7 +17,7 @@ process SPLIT {
     zcat ${fastq} | split -l 4000000 - ${fastq.simpleName}_
 
     ls -l ${fastq.simpleName}_* | \\
-        awk '{system("if [\$((wc -l "\$9")) -ne 4000000]; then exit 1; fi")}'
+        awk '{system("if [\$(wc -l "\$9") -ne 4000000]; then exit 1; fi")}'
 
     ls -l ${fastq.simpleName}_* | \\
         awk '{system("gzip -c "\$9" > "\$9".fastq.gz && rm "\$9)}'