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Commit bf8af308 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch '89-badges' into 'develop' 

Resolve "Add tool version badges"

Closes #88 and #89

See merge request !55
parents 3f23ba95 c90de001
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2 merge requests!58Develop,!55Resolve "Add tool version badges"
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.gitlab-ci.yml
+ 33
− 6
View file @ bf8af308
......@@ -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"
......
README.md
+ 2
− 2
View file @ bf8af308
|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]()]()
......
workflow/rna-seq.nf
+ 5
− 3
View file @ bf8af308
......@@ -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:
......
workflow/scripts/get_updated_badge_info.sh
+ 30
− 8
View file @ bf8af308
......@@ -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
workflow/scripts/get_updated_rep_count.sh 0 → 100644
+ 24
− 0
View file @ bf8af308
#!/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
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