split.nf: change detection of file truncation

src/modules/split.nf

@@ -17,11 +17,17 @@ 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 echo "1" > error.txt; fi")}'
 
     ls -l ${fastq.simpleName}_* | \\
         awk '{system("gzip -c "\$9" > "\$9".fastq.gz && rm "\$9)}'
 
+    if [ -e "error.txt" ]
+    then 
+        echo "file truncation detected" >&2
+        exit 1
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         split: v1.35.0