Add force params for stranded and spike

.gitlab-ci.yml

@@ -660,11 +660,11 @@ integration_se:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source dev --upload true -with-dag dag.png --dev false --ci true --email 'venkat.malladi@utsouthwestern.edu,Gervaise.Henry@UTSouthwestern.edu'
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source dev --upload true -with-dag dag.png --dev false --ci true -with-report ./SE_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -684,11 +684,11 @@ integration_pe:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source dev --upload true -with-dag dag.png --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source dev --upload true -with-dag dag.png --dev false --ci true -with-report ./PE_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -710,11 +710,11 @@ failAmbiguousSpecies:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source dev --upload true -with-dag dag.png --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source dev --upload true -with-dag dag.png --dev false --ci true -with-report ./failAmbiguousSpecies_report.html
   retry:
     max: 0
     when:
@@ -725,11 +725,11 @@ failTrunkation:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source dev --upload true -with-dag dag.png --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source dev --upload true -with-dag dag.png --dev false --ci true -with-report ./failTrunkation_report.html
   retry:
     max: 0
     when:
@@ -740,11 +740,11 @@ failMismatchR1R2:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source dev --upload true -with-dag dag.png --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source dev --upload true -with-dag dag.png --dev false --ci true -with-report ./failMismatchR1R2_report.html
   retry:
     max: 0
     when:
@@ -755,11 +755,11 @@ failUnexpectedMeta:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source dev --upload true -with-dag dag.png --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source dev --upload true -with-dag dag.png --dev false --ci true -with-report ./failUnexpectedMeta_report.html
   retry:
     max: 0
     when:
@@ -770,11 +770,11 @@ failFileStructure:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source dev --upload true -with-dag dag.png --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source dev --upload true -with-dag dag.png --dev false --ci true -with-report ./failFileStructure_report.html
   retry:
     max: 0
     when:
@@ -785,11 +785,11 @@ override_inputBag:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source dev --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source dev --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true -with-report ./inputBagOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -807,11 +807,11 @@ override_fastq:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source dev --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source dev --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true -with-report ./fastqOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -829,11 +829,11 @@ override_species:
   only: [merge_requests]
   except:
     variables:
-        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source dev --speciesForce 'Homo sapiens' --upload false --dev false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source dev --speciesForce 'Homo sapiens' --upload false --dev false --ci true -with-report ./speciesOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -846,6 +846,50 @@ override_species:
     when:
       - always
 
+override_stranded:
+  stage: integration
+  only: [merge_requests]
+  except:
+    variables:
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+  script:
+  - hostname
+  - ulimit -a
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source dev --strandedForce unstranded --upload false --dev false --ci true -with-report ./strandedOverride_report.html
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_PE_multiqc_data.json \;
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - strandedOverride_PE_multiqc_data.json
+    expire_in: 7 days
+  retry:
+    max: 0
+    when:
+      - always
+
+override_stpike:
+  stage: integration
+  only: [merge_requests]
+  except:
+    variables:
+      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+  script:
+  - hostname
+  - ulimit -a
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source dev --spikeForce t --upload false --dev false --ci true -with-report ./spikeOverride_report.html
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_PE_multiqc_data.json \;
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - spikedOverride_PE_multiqc_data.json
+    expire_in: 7 days
+  retry:
+    max: 0
+    when:
+      - always
+
 
 consistency:
   stage: consistency

CHANGELOG.md

@@ -3,6 +3,7 @@
 * Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility)
 * Strandedness metadata "yes"/"no" changed to boolean "t"/"f" in data-hub, pipeline updated to handle (#70) ("yes"/"no" still acceptable for backwards compatibility)
 * Upload empty mRNA_QC entry if data error (#111)
+* Allow forcing of strandedness and spike (#100)
 
 **Background**
 * Add memory limit (75%) per thread for samtools sort (#108)

README.md

@@ -57,8 +57,12 @@ To Run:
     * eg: `--inputBagForce test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip` (must be the expected bag structure, this example will not work because it is a test bag)
   * `--fastqsForce` utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)
     * eg: `--fastqsForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz'` (note the quotes around fastq's which must me named in the correct standard [*\*.R1.fastq.gz and/or \*.R2.fastq.gz*] and in the correct order)
-  * `--speciesForce` forces the species to be "Mus musculus" or "Homo sapiens", it bypasses ambiguous species error
+  * `--speciesForce` forces the species to be "Mus musculus" or "Homo sapiens", it bypasses a metadata mismatch or an ambiguous species error
     * eg: `--speciesForce 'Mus musculus'`
+  * `--strandedForce` forces the strandedness to be "forward", "reverse" or "unstranded", it bypasses a metadata mismatch error
+    * eg: `--strandedForce 'unstranded'`
+  * `--spikeForce` forces the spike-in to be "f" or "t", it bypasses a metadata mismatch error
+    * eg: `--spikeForce 't'`
 * Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
   * `--ci` boolean (default = false)
   * `--dev` boolean (default = true)

workflow/rna-seq.nf

@@ -27,6 +27,8 @@ params.refSource = "biohpc"
 params.inputBagForce = ""
 params.fastqsForce = ""
 params.speciesForce = ""
+params.strandedForce = ""
+params.spikeForce = ""
 
 // Define tracking input variables
 params.ci = false
@@ -64,6 +66,8 @@ upload = params.upload
 inputBagForce = params.inputBagForce
 fastqsForce = params.fastqsForce
 speciesForce = params.speciesForce
+sptrandedForce = params.speciesForce
+spikeForce = params.speciesForce
 email = params.email
 
 // Define fixed files and variables
@@ -311,6 +315,8 @@ process parseMetadata {
     path experiment from experimentMeta
     path (fastq) from fastqs_parseMetadata.collect()
     val fastqCount
+    val strandedForce
+    val spikeForce
 
   output:
     path "design.csv" into metadata_fl
@@ -364,10 +370,20 @@ process parseMetadata {
     # get strandedness metadata
     stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p stranded)
     echo -e "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.log
+    if [ "\${strandedForce}" != "" ]
+    then
+      stranded=${strandedForce}
+      echo -e "LOG: spike-in metadata forced: \${spike}" >> ${repRID}.parseMetadata.log
+    fi
 
     # get spike-in metadata
     spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p spike)
     echo -e "LOG: spike-in metadata parsed: \${spike}" >> ${repRID}.parseMetadata.log
+    if [ "\${spikeForce}" != "" ]
+    then
+      spike=${spikeForce}
+      echo -e "LOG: spike-in metadata forced: \${spike}" >> ${repRID}.parseMetadata.log
+    fi
     if [ "\${spike}" == "f" ]
     then
       spike="false"
@@ -1170,51 +1186,68 @@ process checkMetadata {
 
     pipelineError=false
     # check if submitted metadata matches inferred
-    if [ "${endsMeta}" != "${endsInfer}" ]
-    then
-      pipelineError=true
-      pipelineError_ends=true
-      echo -e "LOG: ends do not match: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
-    else
-      pipelineError_ends=false
-      echo -e "LOG: ends matches: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
-    fi
     if [ "${strandedMeta}" != "${strandedInfer}" ]
     then
-      pipelineError=true
-      pipelineError_stranded=true
-      if [ "${strandedMeta}" == "stranded" ]
+      if [ "${params.strandedForce}" != "" ]
       then
-        if [[ "${strandedInfer}" == "forward" ]] || [[ "${strandedInfer}" == "reverse" ]]
+        pipelineError=false
+        echo -e "LOG: stranded forced: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
+      else
+        pipelineError=true
+        pipelineError_stranded=true
+        if [ "${strandedMeta}" == "stranded" ]
         then
-          pipelineError=false
-          pipelineError_stranded=false
-          echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
+          if [[ "${strandedInfer}" == "forward" ]] || [[ "${strandedInfer}" == "reverse" ]]
+          then
+            pipelineError=false
+            pipelineError_stranded=false
+            echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
+          else
+            echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
+          fi
         else
           echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
         fi
-      else
-        echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
       fi
     else
       pipelineError=false
-      pipelineError_stranded=false
       echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
     fi
-    if [ "${spikeMeta}" != "${spikeInfer}" ]
+    if [ "${endsMeta}" != "${endsInfer}" ]
     then
       pipelineError=true
-      pipelineError_spike=true
-      echo -e "LOG: spike does not match: Submitted=${spikeMeta}; Inferred=${spikeInfer}" >> ${repRID}.checkMetadata.log
+      pipelineError_ends=true
+      echo -e "LOG: ends do not match: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
+    else
+      pipelineError_ends=false
+      echo -e "LOG: ends matches: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
+    fi
+    if [ "${spikeMeta}" != "${spikeInfer}" ]
+    then
+      if [[ "${params.spikeForce}" != "" ]]
+      then
+        pipelineError_spike=false
+        echo -e "LOG: spike forced: Submitted=${spikeMeta}; Inferred=${spikeInfer}" >> ${repRID}.checkMetadata.log
+      else
+        pipelineError=true
+        pipelineError_spike=true
+        echo -e "LOG: spike does not match: Submitted=${spikeMeta}; Inferred=${spikeInfer}" >> ${repRID}.checkMetadata.log
+      fi
     else
       pipelineError_spike=false
-      echo -e "LOG: stranded matches: Submitted=${spikeMeta}; Inferred=${spikeInfer}" >> ${repRID}.checkMetadata.log
+      echo -e "LOG: spike matches: Submitted=${spikeMeta}; Inferred=${spikeInfer}" >> ${repRID}.checkMetadata.log
     fi
     if [ "${speciesMeta}" != "${speciesInfer}" ]
     then
-      pipelineError=true
-      pipelineError_species=true
-      echo -e "LOG: species does not match: Submitted=${speciesMeta}; Inferred=${speciesInfer}" >> ${repRID}.checkMetadata.log
+    if [[ "${params.speciesForce}" != "" ]]
+      then
+        pipelineError_species=false
+        echo -e "LOG: species forced: Submitted=${speciesMeta}; Inferred=${speciesInfer}" >> ${repRID}.checkMetadata.log
+      else
+        pipelineError=true
+        pipelineError_species=true
+        echo -e "LOG: species does not match: Submitted=${speciesMeta}; Inferred=${speciesInfer}" >> ${repRID}.checkMetadata.log
+      fi
     else
       pipelineError_species=false
       echo -e "LOG: species matches: Submitted=${speciesMeta}; Inferred=${speciesInfer}" >> ${repRID}.checkMetadata.log
@@ -1935,7 +1968,7 @@ process aggrQC {
     ulimit -a >> ${repRID}.aggrQC.log
 
     # make run table
-    if [ "${params.inputBagForce}" == "" ] && [ "${params.fastqsForce}" == "" ] && [ "${params.speciesForce}" == "" ]
+    if [ "${params.inputBagForce}" == "" ] && [ "${params.fastqsForce}" == "" ] && [ "${params.speciesForce}" == "" && [ "${params.strandedForce}" == "" && [ "${params.spikeForce}" == "" ]
     then
       input="default"
     else
@@ -1952,6 +1985,14 @@ process aggrQC {
       then
         input=\$(echo \${input} species)
       fi
+      if [ "${params.strandedForce}" != "" ]
+      then
+        input=\$(echo \${input} stranded)
+      fi
+      if [ "${params.spikeForce}" != "" ]
+      then
+        input=\$(echo \${input} spike)
+      fi
     fi
     echo -e "LOG: creating run table" >> ${repRID}.aggrQC.log
     echo -e "Session\tSession ID\tStart Time\tPipeline Version\tInput" > run.tsv
@@ -1969,10 +2010,24 @@ process aggrQC {
     echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t-\t'${readLengthM}'\t-" >> metadata.tsv
     if [ "${params.speciesForce}" == "" ]
     then
-      echo -e "Inferred\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
+      input=\$(echo "Inferred\t${speciesI}\t)
+    else
+      input=\${echo "Inferred\t${speciesI} (FORCED)\t)
+    fi
+    input=\$(echo \${input}${endsI}\t)
+    if [ "${params.strandedForce}" == "" ]
+    then
+      input=\$(echo \${input}${strandedI}\t)
     else
-      echo -e "Inferred\t${speciesI} (FORCED)\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
+      input=$(echo \${input}${strandedI} (FORCED)\t)
     fi
+    if [ "${params.spikeForce}" == "" ]
+    then
+      input=$(echo \${input}${spikeI}\t-\t-\t-\t-)
+    else
+      input=$(echo \${input}${spikeI} (FORCED)\t-\t-\t-\t-" >> metadata.tsv
+    fi
+    echo -e \${input} >> metadata.tsv
     echo -e "Measured\t-\t${endsManual}\t-\t-\t'${rawReadsI}'\t'${assignedReadsI}'\t'${readLengthI}'\t'${tinMedI}'" >> metadata.tsv
 
     # make reference table
@@ -2231,11 +2286,11 @@ process uploadOutputBag {
     echo LOG: output bag RID uploaded - \${outputBag_rid} >> ${repRID}.uploadOutputBag.log
     rid=\${outputBag_rid}
   else
-      exist=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
-      exist=\${exist:8:-6}
-      outputBag_rid=\$(python3 ${script_uploadOutputBag} -e ${executionRunRID} -o ${source} -c \${cookie} -u \${exist})
-      echo LOG: output bag RID already exists - \${exist} >> ${repRID}.uploadOutputBag.log
-      rid=\${exist}
+    exist=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
+    exist=\${exist:8:-6}
+    outputBag_rid=\$(python3 ${script_uploadOutputBag} -e ${executionRunRID} -o ${source} -c \${cookie} -u \${exist})
+    echo LOG: output bag RID already exists - \${exist} >> ${repRID}.uploadOutputBag.log
+    rid=\${exist}
   fi
 
   echo "\${rid}" > outputBagRID.csv