Merge branch 'develop' into '11-deriva.upload'

# Conflicts:
#   .gitlab-ci.yml

.gitlab-ci.yml

@@ -13,12 +13,35 @@ variables:
   refERCCVersion: "92"
 
 stages:
+  - badges
+  - deploy
   - unit
   - aggregation
   - reference
   - integration
   - consistency
 
+build_badges:
+  stage: badges
+  before_script:
+    - module load singularity/3.5.3
+    - chmod +x get-updated-badge-info.sh
+  script:
+    - echo "Building badges"
+    - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash get-updated-badge-info.sh
+  artifacts:
+    paths:
+      - badges/
+
+pages:
+  stage: deploy
+  dependencies:
+    - build_badges
+  script:
+    - mv badges/ public/
+  artifacts:
+    paths:
+    - public
 
 getBag:
   stage: unit

README.md

-|*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)|
+|tag|master|develop|
+|:-:|:-:|:-:|
+|![release](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/release.svg)|[![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/releasePipeline.svg)|![pipeline](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/masterPipeline.svg)|![pipeline](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/developPipeline.svg)|
+|![nextflow](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/releaseNextflow.svg)|![nextflow](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/masterNextflow.svg)|![nextflow](https://gudmap_rbk.pages.biohpc.swmed.edu/rna-seq/developNextflow.svg)|
+
 <!--
 [![DOI]()]()
 -->

get-updated-badge-info.sh

+#!/bin/bash
+
+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 =" ${develop_nextflow_version}
+
+echo "collecting badges"
+mkdir badges
+curl --request GET https://img.shields.io/badge/Latest%20Release-${latest_release_tag}-green?style=flat > ./badges/release.svg
+curl --request GET https://img.shields.io/badge/Pipeline%20Version-${current_pipeline_version}-green?style=flat > ./badges/releasePipeline.svg
+curl --request GET https://img.shields.io/badge/Nextflow%20Version-${current_nextflow_version}-green?style=flat > ./badges/releaseNextflow.svg
+curl --request GET https://img.shields.io/badge/Pipeline%20Version-${master_pipeline_version}-green?style=flat > ./badges/masterPipeline.svg
+curl --request GET https://img.shields.io/badge/Nextflow%20Version-${master_nextflow_version}-green?style=flat > ./badges/masterNextflow.svg
+curl --request GET https://img.shields.io/badge/Pipeline%20Version-${develop_pipeline_version}-green?style=flat > ./badges/developPipeline.svg
+curl --request GET https://img.shields.io/badge/Nextflow%20Version-${develop_nextflow_version}-green?style=flat > ./badges/developNextflow.svg
\ No newline at end of file