diff --git a/workflow/scripts/get_updated_badge_info.sh b/workflow/scripts/get_updated_badge_info.sh index fb230c4a2fc47c64340cc42fafc4c5e032e06a41..48879f4b14dad9a3c95b6d5d1edd73f8976173d0 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 ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o Python.* | grep -oP "(?<=d>).*(?=\<)") -deriva_version=$(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 ${latest_release_tag}:docs/software_versions_mqc.yaml | grep -o MultiQC.* | grep -oP "(?<=d>).*(?=\<)") +python_version=$(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>).*(?=\<)") echo "collecting badges" mkdir -p ./badges/tools