From a89eb9f510542df6187a345d919cfb91a7e17af4 Mon Sep 17 00:00:00 2001 From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu> Date: Fri, 20 Nov 2020 10:42:35 -0600 Subject: [PATCH] Add Jons Syntax Fix --- workflow/rna-seq.nf | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 0e288f9..04709a1 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -1248,15 +1248,17 @@ process outputBag { echo -e "**Workflow URL:** https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq" >> runDetails.md echo -e "**Workflow Version:** ${workflow.manifest.version}" >> runDetails.md echo -e "**Description:** ${workflow.manifest.description}" >> runDetails.md - if [ "${species}" == "Mus musculus" ] - then - echo -e "**Genome Assembly Version:** GRCm38 patch p6" >> runDetails.md - echo -e "**Annotation Version:** GENCODE release M22" >> runDetails.md - elif [ "${species}" == "Homo sapiens" ] - then - echo -e "**Genome Assembly Version:** GRCh38 patch p12" >> runDetails.md - echo -e "**Annotation Version:** GENCODE release 31" >> runDetails.md + if [ "${species}" == "Mus musculus" ]; then + genome=\$(echo GRCm${refMoVersion} | cut -d '.' -f1) + patch=\$(echo ${refMoVersion} | cut -d '.' -f2) + annotation=\$(echo ${refMoVersion} | cut -d '.' -f3 | tr -d 'v') + elif [ "${species}" == "Homo sapiens" ]; then + genome=\$(echo GRCh${refHuVersion} | cut -d '.' -f1) + patch=\$(echo ${refHuVersion} | cut -d '.' -f2) + annotation=\$(echo ${refHuVersion} | cut -d '.' -f3 | tr -d 'v') fi + echo -e "**Genome Assembly Version:** \${genome} patch \${patch}" >> runDetails.md + echo -e "**Annotation Version:** GENCODE release \${annotation}" >> runDetails.md echo -e "**Run ID:** ${repRID}" >> runDetails.md cp runDetails.md Replicate_${repRID}.outputBag cp ${multiqc} Replicate_${repRID}.outputBag -- GitLab