Collect tool version badges

.gitlab-ci.yml

@@ -23,10 +23,6 @@ stages:
 
 build_badges:
   stage: badges
-  only:
-    - master
-    - develop
-    - tags
   before_script:
     - module load singularity/3.5.3
     - chmod +x ./workflow/scripts/get_updated_badge_info.sh
@@ -39,14 +35,11 @@ build_badges:
 
 pages:
   stage: deploy
-  only:
-    - master
-    - develop
-    - tags
   dependencies:
     - build_badges
   script:
-    - mv badges/ public/
+    - mkdir -p public/badges
+    - mv badges/ public/badges/
   artifacts:
     paths:
     - public

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 ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o Python.* | grep -oP "(?<=d>).*(?=\<)")
+deriva_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o DERIVA.* | grep -oP "(?<=d>).*(?=\<)")
+bdbag_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o BDBag.* | grep -oP "(?<=d>).*(?=\<)")
+rseqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o RSeQC.* | grep -oP "(?<=d>).*(?=\<)")
+trimgalore_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o 'Trim Galore!'.* | grep -oP "(?<=d>).*(?=\<)")
+hisat2_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o HISAT2.* | grep -oP "(?<=d>).*(?=\<)")
+samtools_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o Samtools.* | grep -oP "(?<=d>).*(?=\<)")
+picard_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o 'picard (MarkDuplicates)'.* | grep -oP "(?<=d>).*(?=\<)")
+featurecounts_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o featureCounts.* | grep -oP "(?<=d>).*(?=\<)")
+r_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o R.* | grep -oP "(?<=d>).*(?=\<)")
+deeptools_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o deepTools.* | grep -oP "(?<=d>).*(?=\<)")
+fastqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o FastQC.* | grep -oP "(?<=d>).*(?=\<)")
+multiqc_version=$(git show ${latest_release_tag}: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}-informational?style=flat > ./badges/tools/python.svg
+curl --request GET https://img.shields.io/badge/DERIVA%20Version-${deriva_version}-informational?style=flat > ./badges/tools/deriva.svg
+curl --request GET https://img.shields.io/badge/BDBag%20Version-${bdbag_version}-informational?style=flat > ./badges/tools/bdbag.svg
+curl --request GET https://img.shields.io/badge/RSeQC%20Version-${rseqc_version}-informational?style=flat > ./badges/tools/rseqc.svg
+curl --request GET https://img.shields.io/badge/Trim%20Galore%20Version-${trimgalore_version}-informational?style=flat > ./badges/tools/trimgalore.svg
+curl --request GET https://img.shields.io/badge/HISAT2%20Version-${hisat2_version}-informational?style=flat > ./badges/tools/hisat2.svg
+curl --request GET https://img.shields.io/badge/Samtools%20Version-${samtools_version}-informational?style=flat > ./badges/tools/samtools.svg
+curl --request GET https://img.shields.io/badge/picard%20Version-${picard_version}-informational?style=flat > ./badges/tools/picard.svg
+curl --request GET https://img.shields.io/badge/featureCounts%20Version-${featurecounts_version}-informational?style=flat > ./badges/tools/featurecounts.svg
+curl --request GET https://img.shields.io/badge/R%20Version-${r_version}-informational?style=flat > ./badges/tools/r.svg
+curl --request GET https://img.shields.io/badge/deepTools%20Version-${deeptools_version}-informational?style=flat > ./badges/tools/deeptools.svg
+curl --request GET https://img.shields.io/badge/FastQC%20Version-${fastqc_version}-informational?style=flat > ./badges/tools/fastqc.svg
+curl --request GET https://img.shields.io/badge/MultiQC%20Version-${multiqc_version}-informational?style=flat > ./badges/tools/multiqc.svg
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