diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b924a7431d02ddd74e88341077a90a639bf793f4..b0131c6ff424bf4002075c28dcf6e6cbb207536c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -33,6 +33,7 @@ build_badges:
   script:
     - echo "Building badges"
     - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_badge_info.sh
+    - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_rep_count.sh
   artifacts:
     paths:
       - badges/
@@ -46,7 +47,8 @@ pages:
   dependencies:
     - build_badges
   script:
-    - mv badges/ public/
+    - mkdir -p public
+    - mv badges/ public/badges/
   artifacts:
     paths:
     - public
@@ -58,6 +60,7 @@ getBag:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
   - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli --version > version_deriva.txt
@@ -77,6 +80,7 @@ getData:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - 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
@@ -97,6 +101,7 @@ parseMetadata:
     - tags
   except:
     - merge_requests
+    - schedules
   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/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
@@ -124,6 +129,7 @@ inferMetadata:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
   - >
@@ -148,6 +154,7 @@ trimData:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
   - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
@@ -169,6 +176,7 @@ downsampleData:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
   - pytest -m downsampleData
@@ -180,6 +188,7 @@ alignData:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 --version > version_hisat2.txt
   - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools --version > version_samtools.txt
@@ -207,6 +216,7 @@ dedupData:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools --version > version_samtools.txt
   - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
@@ -233,6 +243,7 @@ countData:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv
   - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv
@@ -258,6 +269,7 @@ makeBigWig:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
   - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
@@ -276,6 +288,7 @@ fastqc:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
   - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
@@ -310,6 +323,7 @@ uploadInputBag:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
   - echo THIS IS A TEST FILE > test.txt
@@ -336,6 +350,7 @@ uploadExecutionRun:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
   - >
@@ -359,6 +374,7 @@ uploadQC:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
   - >
@@ -382,6 +398,7 @@ uploadProcessedFile:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
   - echo THIS IS A TEST FILE > 17-BTFJ_test.csv
@@ -412,6 +429,7 @@ uploadOutputBag:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
   - echo THIS IS A TEST FILE > test.txt
@@ -439,6 +457,7 @@ generateVersions:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
   - python ./workflow/scripts/generate_versions.py -o software_versions
@@ -459,6 +478,7 @@ human_BioHPC:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - mkdir -p hu
   - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/
@@ -470,6 +490,7 @@ mouse_BioHPC:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - mkdir -p mo
   - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/
@@ -481,6 +502,7 @@ human_dev:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - referenceBase=dev.gudmap.org
@@ -506,6 +528,7 @@ mouse_dev:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - referenceBase=dev.gudmap.org
@@ -531,6 +554,7 @@ human_staging:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - referenceBase=staging.gudmap.org
@@ -556,6 +580,7 @@ mouse_staging:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - referenceBase=staging.gudmap.org
@@ -582,6 +607,7 @@ human_prod:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - referenceBase=www.gudmap.org
@@ -607,6 +633,7 @@ mouse_prod:
     - tags
   except:
     - merge_requests
+    - schedules
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - referenceBase=www.gudmap.org
@@ -636,7 +663,7 @@ integration_se:
   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 -with-dag dag.png --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 staging -with-dag dag.png --dev false --ci true --email 'venkat.malladi@utsouthwestern.edu,Gervaise.Henry@UTSouthwestern.edu'
   - find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -660,7 +687,7 @@ integration_pe:
   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 -with-dag dag.png --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 staging -with-dag dag.png --dev false --ci true
   - find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -686,7 +713,7 @@ override_inputBag:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true
   - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -708,7 +735,7 @@ override_fastq:
   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 --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload 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 staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true
   - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -730,7 +757,7 @@ override_species:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --speciesForce 'Homo sapiens' --upload false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --speciesForce 'Homo sapiens' --upload false --dev false --ci true
   - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
diff --git a/README.md b/README.md
index 2b558d72173309c71fd6c7c83d1a52f5470825d8..185f4453163575fc4b76e8ccb00aac53c74b25ab 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
 |master|develop|
 |:-:|:-:|
 |[![pipeline status](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/commits/master)|[![pipeline status](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/badges/develop/pipeline.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/commits/develop)|
-|[![pipeline](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/masterPipeline.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/master)|[![pipeline](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/developPipeline.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/develop)|
-|[![nextflow](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/masterNextflow.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/master)|[![nextflow](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/developNextflow.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/develop)|
+|[![pipeline](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/badges/masterPipeline.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/master)|[![pipeline](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/badges/developPipeline.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/develop)|
+|[![nextflow](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/badges/masterNextflow.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/master)|[![nextflow](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/badges/developNextflow.svg)](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tree/develop)|
 
 <!--
 [![DOI]()]()
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index bd1aee4ea8fda6acce19febbec38e0118ed0079b..3a97735fe88059a99de264e03d798dc5e2410032 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -18,7 +18,7 @@ params.refMoVersion = "38.p6.vM22"
 params.refHuVersion = "38.p12.v31"
 params.refERCCVersion = "92"
 params.outDir = "${baseDir}/../output"
-params.upload = true
+params.upload = false
 params.email = ""
 
 
@@ -28,6 +28,10 @@ params.inputBagForce = ""
 params.fastqsForce = ""
 params.speciesForce = ""
 
+// Define tracking input variables
+params.ci = false
+params.dev = true
+
 
 // Parse input variables
 deriva = Channel
@@ -100,8 +104,6 @@ script_deleteEntry_uploadProcessedFile = Channel.fromPath("${baseDir}/scripts/de
 /*
  * trackStart: track start of pipeline
  */
-params.ci = false
-params.dev = false
 process trackStart {
   container 'docker://bicf/bicfbase:2.1.0'
   script:
diff --git a/workflow/scripts/get_updated_badge_info.sh b/workflow/scripts/get_updated_badge_info.sh
index 05a08dc7a6056498f73d26f4dc8cdedd3db58f84..5081fe2716af90f5ec4987a8c6f317a4ca08f7aa 100644
--- a/workflow/scripts/get_updated_badge_info.sh
+++ b/workflow/scripts/get_updated_badge_info.sh
@@ -2,22 +2,30 @@
 
 echo "collecting stats for badges"
 latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1)
-echo "latest_release_tag =" ${latest_release_tag}
 current_pipeline_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
-echo "current_pipeline_version =" ${current_pipeline_version}
 current_nextflow_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
-echo "current_nextflow_version =" ${current_nextflow_version}
 master_pipeline_version=$(git show origin/master:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
-echo "master_pipeline_version =" ${master_pipeline_version}
 master_nextflow_version=$(git show origin/master:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
-echo "master_nextflow_version =" ${master_nextflow_version}
 develop_pipeline_version=$(git show origin/develop:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
-echo "develop_pipeline_version =" ${develop_pipeline_version}
 develop_nextflow_version=$(git show origin/develop:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
-echo "develop_nextflow_version =" ${develop_nextflow_version}
+
+echo "collecting tool version for badges"
+python_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o Python.* | grep -oP "(?<=d>).*(?=\<)")
+deriva_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o DERIVA.* | grep -oP "(?<=d>).*(?=\<)")
+bdbag_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o BDBag.* | grep -oP "(?<=d>).*(?=\<)")
+rseqc_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o RSeQC.* | grep -oP "(?<=d>).*(?=\<)")
+trimgalore_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o 'Trim Galore!'.* | grep -oP "(?<=d>).*(?=\<)")
+hisat2_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o HISAT2.* | grep -oP "(?<=d>).*(?=\<)")
+samtools_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o Samtools.* | grep -oP "(?<=d>).*(?=\<)")
+picard_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o 'picard (MarkDuplicates)'.* | grep -oP "(?<=d>).*(?=\<)")
+featurecounts_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o featureCounts.* | grep -oP "(?<=d>).*(?=\<)")
+r_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o '>R<'.* | grep -oP "(?<=d>).*(?=\<)")
+deeptools_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o deepTools.* | grep -oP "(?<=d>).*(?=\<)")
+fastqc_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o FastQC.* | grep -oP "(?<=d>).*(?=\<)")
+multiqc_version=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o MultiQC.* | grep -oP "(?<=d>).*(?=\<)")
 
 echo "collecting badges"
-mkdir badges
+mkdir -p ./badges/tools
 curl --request GET https://img.shields.io/badge/Latest%20Release-${latest_release_tag}-informational?style=flat > ./badges/release.svg
 curl --request GET https://img.shields.io/badge/Pipeline%20Version-${current_pipeline_version}-informational?style=flat > ./badges/releasePipeline.svg
 curl --request GET https://img.shields.io/badge/Nextflow%20Version-${current_nextflow_version}-informational?style=flat > ./badges/releaseNextflow.svg
@@ -25,3 +33,17 @@ curl --request GET https://img.shields.io/badge/Pipeline%20Version-${master_pipe
 curl --request GET https://img.shields.io/badge/Nextflow%20Version-${master_nextflow_version}-informational?style=flat > ./badges/masterNextflow.svg
 curl --request GET https://img.shields.io/badge/Pipeline%20Version-${develop_pipeline_version}-informational?style=flat > ./badges/developPipeline.svg
 curl --request GET https://img.shields.io/badge/Nextflow%20Version-${develop_nextflow_version}-informational?style=flat > ./badges/developNextflow.svg
+
+curl --request GET https://img.shields.io/badge/Python%20Version-${python_version}-blueviolet?style=flat > ./badges/tools/python.svg
+curl --request GET https://img.shields.io/badge/DERIVA%20Version-${deriva_version}-blueviolet?style=flat > ./badges/tools/deriva.svg
+curl --request GET https://img.shields.io/badge/BDBag%20Version-${bdbag_version}-blueviolet?style=flat > ./badges/tools/bdbag.svg
+curl --request GET https://img.shields.io/badge/RSeQC%20Version-${rseqc_version}-blueviolet?style=flat > ./badges/tools/rseqc.svg
+curl --request GET https://img.shields.io/badge/Trim%20Galore%20Version-${trimgalore_version}-blueviolet?style=flat > ./badges/tools/trimgalore.svg
+curl --request GET https://img.shields.io/badge/HISAT2%20Version-${hisat2_version}-blueviolet?style=flat > ./badges/tools/hisat2.svg
+curl --request GET https://img.shields.io/badge/Samtools%20Version-${samtools_version}-blueviolet?style=flat > ./badges/tools/samtools.svg
+curl --request GET https://img.shields.io/badge/picard%20Version-${picard_version}-blueviolet?style=flat > ./badges/tools/picard.svg
+curl --request GET https://img.shields.io/badge/featureCounts%20Version-${featurecounts_version}-blueviolet?style=flat > ./badges/tools/featurecounts.svg
+curl --request GET https://img.shields.io/badge/R%20Version-${r_version}-blueviolet?style=flat > ./badges/tools/r.svg
+curl --request GET https://img.shields.io/badge/deepTools%20Version-${deeptools_version}-blueviolet?style=flat > ./badges/tools/deeptools.svg
+curl --request GET https://img.shields.io/badge/FastQC%20Version-${fastqc_version}-blueviolet?style=flat > ./badges/tools/fastqc.svg
+curl --request GET https://img.shields.io/badge/MultiQC%20Version-${multiqc_version}-blueviolet?style=flat > ./badges/tools/multiqc.svg
\ No newline at end of file
diff --git a/workflow/scripts/get_updated_rep_count.sh b/workflow/scripts/get_updated_rep_count.sh
new file mode 100644
index 0000000000000000000000000000000000000000..267b4e1bdb5d84a045156abc779e30d739a3616e
--- /dev/null
+++ b/workflow/scripts/get_updated_rep_count.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+echo "collecting stats for badges"
+latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1)
+current_pipeline_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
+
+echo "collecting workflow RIDs from servers"
+dev_workflow_RID=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version=${current_pipeline_version} | grep -o '\"RID\":\".*\",\"RCT')
+dev_workflow_RID=${dev_workflow_RID:7:-6}
+staging_workflow_RID=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version=${current_pipeline_version} | grep -o '\"RID\":\".*\",\"RCT')
+staging_workflow_RID=${staging_workflow_RID:7:-6}
+prod_workflow_RID=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version=${current_pipeline_version} | grep -o '\"RID\":\".*\",\"RCT')
+prod_workflow_RID=${prod_workflow_RID:7:-6}
+
+echo "collecting unique replicates with successful execution runs"
+dev_count=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${dev_workflow_RID} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l)
+staging_count=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${staging_workflow_RID} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l)
+prod_count=$(curl -s https://prod.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${prod_workflow_RID} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l)
+
+echo "collecting badges"
+mkdir -p ./badges/counts
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${dev_count}-lightgrey?style=flat > ./badges/counts/dev_counts.svg
+curl --request GET https://img.shields.io/badge/Staging%20Replicate%20Count-${staging_count}-lightgrey?style=flat > ./badges/counts/staging_counts.svg
+curl --request GET https://img.shields.io/badge/Production%20Replicate%20Count-${prod_count}-lightgrey?style=flat > ./badges/counts/prod_counts.svg