Send delete entry script to upload qc process

.gitlab-ci.yml

@@ -358,7 +358,7 @@ uploadProcessedFile:
     cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
     cookie=${cookie:11:-1} &&
     if [ "${exist}" != "[]" ]; then
-      rids=$(echo $exist | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
+      rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
       for rid in ${rids}; do
         singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t Processed_File -o $staging.gudmap.org -c ${cookie}
         echo old processed file RID deleted - ${rid}

workflow/rna-seq.nf

@@ -94,6 +94,7 @@ script_uploadInputBag = Channel.fromPath("${baseDir}/scripts/uploadInputBag.py")
 script_uploadExecutionRun = Channel.fromPath("${baseDir}/scripts/uploadExecutionRun.py")
 script_uploadQC = Channel.fromPath("${baseDir}/scripts/uploadQC.py")
 script_uploadOutputBag = Channel.fromPath("${baseDir}/scripts/uploadOutputBag.py")
+script_deleteEntry = Channel.fromPath("${baseDir}/scripts/deleteEntry.py")
 
 /*
  * trackStart: track start of pipeline
@@ -1429,6 +1430,7 @@ process uploadQC {
   tag "${repRID}"
 
   input:
+    path script_deleteEntry
     path script_uploadQC
     path credential, stageAs: "credential.json" from deriva_uploadQC
     val executionRunRID from executionRunRID_uploadQC
@@ -1438,6 +1440,7 @@ process uploadQC {
     val rawCount from rawReadsInfer_uploadQC
     val finalCount from assignedReadsInfer_uploadQC
     
+    
   output:
     path ("qcRID.csv") into qcRID_fl