Change python and bash scripts to new naming convention

.gitlab-ci.yml

@@ -50,7 +50,7 @@ getData:
   - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - unzip ./test_data/bag/Q-Y5F6_inputBag.zip
-  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST
   - pytest -m getData
   artifacts:
     name: "$CI_JOB_NAME"
@@ -68,15 +68,15 @@ parseMetadata:
     - merge_requests
   script:
   - singularity run 'docker://gudmaprbk/python3:1.0.0' python3 --version > version_python.txt
-  - rep=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
-  - exp=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
-  - study=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
-  - endsMeta=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
-  - endsManual=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual)
-  - stranded=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
-  - spike=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
-  - species=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
-  - readLength=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
+  - rep=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
+  - exp=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
+  - study=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
+  - endsMeta=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
+  - endsManual=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual)
+  - stranded=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
+  - spike=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
+  - species=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
+  - readLength=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
   - echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
   - pytest -m parseMetadata
   artifacts:
@@ -100,7 +100,7 @@ inferMetadata:
     if [[ ${align} == "" ]]; then exit 1; fi
   - >
     singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
-    ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/inferMeta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
+    ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
     if [[ ${ended} == "" ]]; then exit 1; fi
   - pytest -m inferMetadata
   artifacts:
@@ -290,7 +290,7 @@ uploadInputBag:
       cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
       cookie=${cookie:11:-1} &&
       loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt --parents) &&
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o staging.gudmap.org -c ${cookie}) &&
+      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_input_bag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o staging.gudmap.org -c ${cookie}) &&
       echo ${rid} test input bag created
     else
       rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
@@ -312,12 +312,12 @@ uploadExecutionRun:
     cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
     cookie=${cookie:11:-1} &&
     if [ "${exist}" == "[]" ]; then
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 17-BTFJ -w 17-BTFM -g 17-BT50 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
+      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BTFM -g 17-BT50 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
       echo ${rid} test execution run created
     else
       rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
       rid=${rid:7:-6} &&
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 17-BTFJ -w 17-BTFM -g 17-BT50 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
+      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BTFM -g 17-BT50 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
       echo ${rid} test execution run already exists
     fi
 
@@ -337,11 +337,11 @@ uploadQC:
     if [ "${exist}" != "[]" ]; then
       rids=$(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 mRNA_QC -o staging.gudmap.org -c ${cookie}
+        singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t mRNA_QC -o staging.gudmap.org -c ${cookie}
       done
       echo all old mRNA QC RIDs deleted
     fi
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 17-BTFJ -e 17-BTG4 -p "Single Read" -s forward -l 35 -w 5 -f 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
+      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BTG4 -p "Single Read" -s forward -l 35 -w 5 -f 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
       echo ${rid} test mRNA QC created
 
 uploadProcessedFile:
@@ -363,7 +363,7 @@ uploadProcessedFile:
     if [ "${exist}" != "[]" ]; then
       rids=$(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}
+        singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie}
       done
       echo all old processed file RIDs deleted
     fi
@@ -392,7 +392,7 @@ uploadOutputBag:
       cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
       cookie=${cookie:11:-1} &&
       loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -e 17-BTG4 -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
+      rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_output_bag.py -e 17-BTG4 -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
       echo ${rid} test output bag created
     else
       rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&

workflow/rna-seq.nf

@@ -82,20 +82,20 @@ softwareReferences = Channel.fromPath("${baseDir}/../docs/software_references_mq
 softwareVersions = Channel.fromPath("${baseDir}/../docs/software_versions_mqc.yaml")
 
 // Define script files
-script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
-script_parseMeta = Channel.fromPath("${baseDir}/scripts/parseMeta.py")
-script_inferMeta = Channel.fromPath("${baseDir}/scripts/inferMeta.sh")
-script_refDataInfer = Channel.fromPath("${baseDir}/scripts/extractRefData.py")
-script_refData = Channel.fromPath("${baseDir}/scripts/extractRefData.py")
+script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbag_fetch.sh")
+script_parseMeta = Channel.fromPath("${baseDir}/scripts/parse_meta.py")
+script_inferMeta = Channel.fromPath("${baseDir}/scripts/infer_meta.sh")
+script_refDataInfer = Channel.fromPath("${baseDir}/scripts/extract_ref_data.py")
+script_refData = Channel.fromPath("${baseDir}/scripts/extract_ref_data.py")
 script_calculateTPM = Channel.fromPath("${baseDir}/scripts/calculateTPM.R")
 script_convertGeneSymbols = Channel.fromPath("${baseDir}/scripts/convertGeneSymbols.R")
-script_tinHist = Channel.fromPath("${baseDir}/scripts/tinHist.py")
-script_uploadInputBag = Channel.fromPath("${baseDir}/scripts/uploadInputBag.py")
-script_uploadExecutionRun = Channel.fromPath("${baseDir}/scripts/uploadExecutionRun.py")
-script_uploadQC = Channel.fromPath("${baseDir}/scripts/uploadQC.py")
-script_uploadOutputBag = Channel.fromPath("${baseDir}/scripts/uploadOutputBag.py")
-script_deleteEntry_uploadQC = Channel.fromPath("${baseDir}/scripts/deleteEntry.py")
-script_deleteEntry_uploadProcessedFile = Channel.fromPath("${baseDir}/scripts/deleteEntry.py")
+script_tinHist = Channel.fromPath("${baseDir}/scripts/tin_hist.py")
+script_uploadInputBag = Channel.fromPath("${baseDir}/scripts/upload_input_bag.py")
+script_uploadExecutionRun = Channel.fromPath("${baseDir}/scripts/upload_execution_run.py")
+script_uploadQC = Channel.fromPath("${baseDir}/scripts/upload_qc.py")
+script_uploadOutputBag = Channel.fromPath("${baseDir}/scripts/upload_output_bag.py")
+script_deleteEntry_uploadQC = Channel.fromPath("${baseDir}/scripts/delete_entry.py")
+script_deleteEntry_uploadProcessedFile = Channel.fromPath("${baseDir}/scripts/delete_entry.py")
 
 /*
  * trackStart: track start of pipeline
@@ -490,9 +490,9 @@ process getRefInfer {
         query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${refName}${refERCCVersion}/Annotation_Version=${refName}${refERCCVersion}')
       fi
       curl --request GET \${query} > refQuery.json
-      refURL=\$(python extractRefData.py --returnParam URL)
+      refURL=\$(python ${script_refDataInfer} --returnParam URL)
       loc=\$(dirname \${refURL})
-      fName=\$(python extractRefData.py --returnParam fName)
+      fName=\$(python ${script_refDataInfer} --returnParam fName)
       fName=\${fName%.*}
       if [ "\${loc}" = "/hatrac/*" ]; then echo "LOG: Reference not present in hatrac"; exit 1; fi
       filename=\$(echo \$(basename \${refURL}) | grep -oP '.*(?=:)')
@@ -682,18 +682,18 @@ process inferMetadata {
     infer_experiment.py -r "\${bed}" -i "\${bam}" 1>> ${repRID}.infer_experiment.txt
     echo -e "LOG: infered" >> ${repRID}.inferMetadata.log
 
-    ended=`bash inferMeta.sh endness ${repRID}.infer_experiment.txt`
-    fail=`bash inferMeta.sh fail ${repRID}.infer_experiment.txt`
+    ended=`bash ${script_inferMeta} endness ${repRID}.infer_experiment.txt`
+    fail=`bash ${script_inferMeta} fail ${repRID}.infer_experiment.txt`
     if [ \${ended} == "PairEnd" ]
     then
       ends="pe"
-      percentF=`bash inferMeta.sh pef ${repRID}.infer_experiment.txt`
-      percentR=`bash inferMeta.sh per ${repRID}.infer_experiment.txt`
+      percentF=`bash ${script_inferMeta} pef ${repRID}.infer_experiment.txt`
+      percentR=`bash ${script_inferMeta} per ${repRID}.infer_experiment.txt`
     elif [ \${ended} == "SingleEnd" ]
     then
       ends="se"
-      percentF=`bash inferMeta.sh sef ${repRID}.infer_experiment.txt`
-      percentR=`bash inferMeta.sh ser ${repRID}.infer_experiment.txt`
+      percentF=`bash ${script_inferMeta} sef ${repRID}.infer_experiment.txt`
+      percentR=`bash ${script_inferMeta} ser ${repRID}.infer_experiment.txt`
     fi
     echo -e "LOG: percentage reads in the same direction as gene: \${percentF}" >> ${repRID}.inferMetadata.log
     echo -e "LOG: percentage reads in the opposite direction as gene: \${percentR}" >> ${repRID}.inferMetadata.log
@@ -840,9 +840,9 @@ process getRef {
       GENCODE=\$(echo \${references} | grep -o \${refName}.* | cut -d '.' -f3)
       query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE})
       curl --request GET \${query} > refQuery.json
-      refURL=\$(python extractRefData.py --returnParam URL)
+      refURL=\$(python ${script_refData} --returnParam URL)
       loc=\$(dirname \${refURL})
-      fName=\$(python extractRefData.py --returnParam fName)
+      fName=\$(python ${script_refData} --returnParam fName)
       fName=\${fName%.*}
       if [ "\${loc}" = "/hatrac/*" ]; then echo "LOG: Reference not present in hatrac"; exit 1; fi
       filename=\$(echo \$(basename \${refURL}) | grep -oP '.*(?=:)')
@@ -1061,11 +1061,11 @@ process countData {
 
     # calculate TPM from the resulting countData table
     echo -e "LOG: calculating TPM with R" >> ${repRID}.countData.log
-    Rscript calculateTPM.R --count "${repRID}_countData"
+    Rscript ${script_calculateTPM} --count "${repRID}_countData"
 
     # convert gene symbols to Entrez id's
     echo -e "LOG: convert gene symbols to Entrez id's" >> ${repRID}.countData.log
-    Rscript convertGeneSymbols.R --repRID "${repRID}"
+    Rscript ${script_convertGeneSymbols} --repRID "${repRID}"
     """
 }
 
@@ -1323,7 +1323,7 @@ process uploadInputBag {
       cookie=\${cookie:11:-1}
 
       loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/input_bag/study/${studyRID}/replicate/${repRID}/\${file} --parents)
-      inputBag_rid=\$(python3 uploadInputBag.py -f \${file} -l \${loc} -s \${md5} -b \${size} -o ${source} -c \${cookie})
+      inputBag_rid=\$(python3 ${script_uploadInputBag} -f \${file} -l \${loc} -s \${md5} -b \${size} -o ${source} -c \${cookie})
       echo LOG: input bag RID uploaded - \${inputBag_rid} >> ${repRID}.uploadInputBag.log
       rid=\${inputBag_rid}
   else
@@ -1397,13 +1397,13 @@ process uploadExecutionRun {
   echo \${exist} >> ${repRID}.uploadExecutionRun.log
   if [ "\${exist}" == "[]" ]
   then
-    executionRun_rid=\$(python3 uploadExecutionRun.py -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s In-progress -d 'Run in process' -o ${source} -c \${cookie} -u F)
+    executionRun_rid=\$(python3 ${script_uploadExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s In-progress -d 'Run in process' -o ${source} -c \${cookie} -u F)
     echo LOG: execution run RID uploaded - \${executionRun_rid} >> ${repRID}.uploadExecutionRun.log
   else
     rid=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
     rid=\${rid:7:-6}
     echo \${rid} >> ${repRID}.uploadExecutionRun.log
-    executionRun_rid=\$(python3 uploadExecutionRun.py -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s In-progress -d 'Run in process' -o ${source} -c \${cookie} -u \${rid})
+    executionRun_rid=\$(python3 ${script_uploadExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s In-progress -d 'Run in process' -o ${source} -c \${cookie} -u \${rid})
     echo LOG: execution run RID updated - \${executionRun_rid} >> ${repRID}.uploadExecutionRun.log
   fi
 
@@ -1470,13 +1470,13 @@ process uploadQC {
     rids=\$(echo \${exist} | grep -o '\\"RID\\":\\".\\{7\\}' | sed 's/^.\\{7\\}//')
     for rid in \${rids}
     do
-      python3 deleteEntry.py -r \${rid} -t mRNA_QC -o ${source} -c \${cookie}
+      python3 ${script_deleteEntry_uploadQC} -r \${rid} -t mRNA_QC -o ${source} -c \${cookie}
       echo LOG: old mRNA QC RID deleted - \${rid} >> ${repRID}.uploadQC.log
     done
     echo LOG: all old mRNA QC RIDs deleted >> ${repRID}.uploadQC.log
   fi
 
-  qc_rid=\$(python3 uploadQC.py -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -o ${source} -c \${cookie} -u F)
+  qc_rid=\$(python3 ${script_deleteEntry_uploadQC} -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -o ${source} -c \${cookie} -u F)
   echo LOG: mRNA QC RID uploaded - \${qc_rid} >> ${repRID}.uploadQC.log
 
   echo \${qc_rid} > qcRID.csv
@@ -1536,7 +1536,7 @@ process uploadProcessedFile {
     rids=\$(echo \${exist} | grep -o '\\"RID\\":\\".\\{7\\}' | sed 's/^.\\{7\\}//')
     for rid in \${rids}
     do
-      python3 deleteEntry.py -r \${rid} -t Processed_File -o ${source} -c \${cookie}
+      python3 ${script_deleteEntry_uploadProcessedFile} -r \${rid} -t Processed_File -o ${source} -c \${cookie}
     done
     echo LOG: all old processed file RIDs deleted >> ${repRID}.uploadQC.log
   fi
@@ -1622,7 +1622,7 @@ process uploadOutputBag {
       cookie=\${cookie:11:-1}
 
       loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/output_bag/study/${studyRID}/replicate/${repRID}/\${file} --parents)
-      outputBag_rid=\$(python3 uploadOutputBag.py -e ${executionRunRID} -f \${file} -l \${loc} -s \${md5} -b \${size} -o ${source} -c \${cookie})
+      outputBag_rid=\$(python3 ${script_uploadOutputBag} -e ${executionRunRID} -f \${file} -l \${loc} -s \${md5} -b \${size} -o ${source} -c \${cookie})
       echo LOG: output bag RID uploaded - \${outputBag_rid} >> ${repRID}.uploadOutputBag.log
       rid=\${outputBag_rid}
   else