Trim - from versions for badge creations

workflow/scripts/get_updated_badge_info.sh

@@ -2,29 +2,29 @@
 
 echo "collecting stats for badges"
 latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1)
-current_pipeline_version=$(git show ${latest_release_tag}:nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
-current_nextflow_version=$(git show ${latest_release_tag}:nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
-master_pipeline_version=$(git show origin/master:nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
-master_nextflow_version=$(git show origin/master:nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
+current_pipeline_version=$(git show ${latest_release_tag}:nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')" | tr "-" _)
+current_nextflow_version=$(git show ${latest_release_tag}:nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')" | tr "-" _)
+master_pipeline_version=$(git show origin/master:nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')" | tr "-" _)
+master_nextflow_version=$(git show origin/master:nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')" | tr "-" _)
 develop_pipeline_version=$(git show origin/develop:nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
-develop_nextflow_version=$(git show origin/develop:nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
+develop_nextflow_version=$(git show origin/develop:nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')" | tr "-" _)
 
 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 ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o BDBag.* | grep -oP "(?<=d>).*(?=\<)")
-trimgalore_version=$(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 ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o featureCounts.* | grep -oP "(?<=d>).*(?=\<)")
-deeptools_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o deepTools.* | grep -oP "(?<=d>).*(?=\<)")
-seqtk_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o Seqtk.* | grep -oP "(?<=d>).*(?=\<)")
-r_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o '>R<'.* | grep -oP "(?<=d>).*(?=\<)")
-fastqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o FastQC.* | grep -oP "(?<=d>).*(?=\<)")
-seqwho_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o SeqWho.* | grep -oP "(?<=d>).*(?=\<)")
-rseqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o RSeQC.* | grep -oP "(?<=d>).*(?=\<)")
-multiqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o MultiQC.* | grep -oP "(?<=d>).*(?=\<)")
+python_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o Python.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+deriva_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o DERIVA.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+bdbag_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o BDBag.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+trimgalore_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o 'Trim Galore!'.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+hisat2_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o HISAT2.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+samtools_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o Samtools.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+picard_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o 'picard (MarkDuplicates)'.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+featurecounts_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o featureCounts.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+deeptools_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o deepTools.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+seqtk_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o Seqtk.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+r_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o '>R<'.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+fastqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o FastQC.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+seqwho_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o SeqWho.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+rseqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o RSeQC.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
+multiqc_version=$(git show ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o MultiQC.* | grep -oP "(?<=d>).*(?=\<)" | tr "-" _)
 
 echo "collecting badges"
 mkdir -p ./badges/tools
@@ -50,4 +50,4 @@ curl --request GET https://img.shields.io/badge/R%20Version-${r_version}-bluevio
 curl --request GET https://img.shields.io/badge/FastQC%20Version-${fastqc_version}-blueviolet?style=flat > ./badges/tools/fastqc.svg
 curl --request GET https://img.shields.io/badge/SeqWho%20Version-${seqwho_version}-blueviolet?style=flat > ./badges/tools/seqwho.svg
 curl --request GET https://img.shields.io/badge/RSeQC%20Version-${rseqc_version}-blueviolet?style=flat > ./badges/tools/rseqc.svg
-curl --request GET https://img.shields.io/badge/MultiQC%20Version-${multiqc_version}-blueviolet?style=flat > ./badges/tools/multiqc.svg
\ No newline at end of file
+curl --request GET https://img.shields.io/badge/MultiQC%20Version-${multiqc_version}-blueviolet?style=flat > ./badges/tools/multiqc.svg