Set fastq count temporarily to zero if overridden

d633e19c · Gervaise Henry · 8f50b748 · d633e19c
Commit d633e19c authored 4 years ago by Gervaise Henry
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -273,6 +273,7 @@ process getData {
      echo -e "LOG: fetched" >> ${repRID}.getData.log
    else
      echo -e "LOG: fastq override detected, not fetching fastqs" >> ${repRID}.getData.log
+      fastqCount="0"
    fi

    if [ "\${fastqCount}" == "0" ]