From b1cdf286e6c92fd3e1f45795e760d10065681b3a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 28 Jan 2021 12:10:43 -0600
Subject: [PATCH] Try excaping tabs for metadata override for report
---
workflow/rna-seq.nf | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index f669989..78a50b1 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -2024,22 +2024,22 @@ process aggrQC {
echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t-\t'${readLengthM}'\t-" >> metadata.tsv
if [ "${params.speciesForce}" == "" ]
then
- input=\$(echo -e "Inferred\t${speciesI}\t")
+ input=\$(echo "Inferred\\t${speciesI}\\t")
else
- input=\$(echo -e "Inferred\t${speciesI} (FORCED)\t")
+ input=\$(echo "Inferred\\t${speciesI} (FORCED)\\t")
fi
- input=\$(echo -e \${input}"${endsI}\t")
+ input=\$(echo \${input}"${endsI}\\t")
if [ "${params.strandedForce}" == "" ]
then
- input=\$(echo -e \${input}"${strandedI}\t")
+ input=\$(echo \${input}"${strandedI}\\t")
else
- input=\$(echo -e \${input}"${strandedI} (FORCED)\t")
+ input=\$(echo \${input}"${strandedI} (FORCED)\\t")
fi
if [ "${params.spikeForce}" == "" ]
then
- input=\$(echo -e \${input}"${spikeI}\t-\t-\t-\t-")
+ input=\$(echo \${input}"${spikeI}\\t-\\t-\\t-\\t-")
else
- input=\$(echo -e \${input}"${spikeI} (FORCED)\t-\t-\t-\t-")
+ input=\$(echo \${input}"${spikeI} (FORCED)\\t-\\t-\\t-\\t-")
fi
echo -e \${input} >> metadata.tsv
echo -e "Measured\t-\t${endsManual}\t-\t-\t'${rawReadsI}'\t'${assignedReadsI}'\t'${readLengthI}'\t'${tinMedI}'" >> metadata.tsv
--
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