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get_updated_badge_info.sh 5.33 KiB
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Create badge json
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#!/bin/bash

echo "collecting stats for badges"
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Fix singularity for badges  
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latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1)
current_pipeline_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
current_nextflow_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
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Check version using remote  
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master_pipeline_version=$(git show origin/master:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
master_nextflow_version=$(git show origin/master:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
develop_pipeline_version=$(git show origin/develop:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
develop_nextflow_version=$(git show origin/develop:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
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Collect tool version badges  
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echo "collecting tool version for badges"
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Change tool versions to query develop because lates tag doesn't have version collecting yet  
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python_version=$(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=$(git show origin/developdocs/software_versions_mqc.yaml | grep -o 'picard (MarkDuplicates)'.* | grep -oP "(?<=d>).*(?=\<)")
featurecounts_version=$(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>).*(?=\<)")
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Change to pulling badges  
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echo "collecting badges"
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Collect tool version badges  
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mkdir -p ./badges/tools
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Update workflow/scripts/get_updated_badge_info.sh, .gitlab-ci.yml files  
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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-${current_nextflow_version}-informational?style=flat > ./badges/releaseNextflow.svg
curl --request GET https://img.shields.io/badge/Pipeline%20Version-${master_pipeline_version}-informational?style=flat > ./badges/masterPipeline.svg
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-${develop_nextflow_version}-informational?style=flat > ./badges/developNextflow.svg
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Collect tool version badges  
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curl --request GET https://img.shields.io/badge/Python%20Version-${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