Catch error if fastq file error grep

workflow/rna-seq.nf

@@ -570,8 +570,8 @@ process fastqc {
 
     # run fastqc
     echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
-    fastqcErrorOut=0
-    fastqc *.fastq.gz -o . &> fastqc.out || fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file')
+    fastqc *.fastq.gz -o . &> fastqc.out || true
+    fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file') || fastqcErrorOut=0
     fastqFileError=false
     fastqFileError_details=""
     if [ "\${fastqcErrorOut}" -ne "0" ]