diff --git a/CHANGELOG.md b/CHANGELOG.md index 206089b5618d4bbfc5396115e4cca79d7005aca6..fb17e5777c467b3a2efbcef27d071e3c4e9bb74c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ **Background** * Change consistency test to check if +/- 1% of standard +* Change tool version checker for badges to use latest tag *Known Bugs* * Override params (inputBag, fastq, species) aren't checked for integrity diff --git a/workflow/scripts/get_updated_badge_info.sh b/workflow/scripts/get_updated_badge_info.sh index 5081fe2716af90f5ec4987a8c6f317a4ca08f7aa..4b929272f2ea80ede5d47b84cd55bad2c6a3fa7b 100644 --- a/workflow/scripts/get_updated_badge_info.sh +++ b/workflow/scripts/get_updated_badge_info.sh @@ -10,19 +10,19 @@ develop_pipeline_version=$(git show origin/develop:workflow/nextflow.config | gr develop_nextflow_version=$(git show origin/develop:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')") 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=$(git show origin/develop:docs/software_versions_mqc.yaml | grep -o MultiQC.* | grep -oP "(?<=d>).*(?=\<)") +python_version=$(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 -p ./badges/tools