From 66da5252d7e8783d7c2ca337f7aa9b1ca41e7923 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 6 Aug 2020 15:57:12 -0500
Subject: [PATCH] Fix tin table in multiqc
---
workflow/conf/multiqc_config.yaml | 10 +++++-----
workflow/rna-seq.nf | 4 ++--
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index 9cf4a9a..5e39335 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -80,11 +80,11 @@ custom_data:
Ends
Stranded
Spike-in
- Raw-Reads
- Assigned-Reads
- Median-Length
- Median-TIN
-
+ Raw Reads
+ Assigned Reads
+ Median Read Length
+ Median TIN
+ tin:
file_format: 'tsv'
section_name: 'TIN'
description: 'This is the distribution of TIN values calculated by the tool RSeQC'
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index f0a63c6..7dd69e5 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1029,7 +1029,7 @@ process aggrQC {
# make metadata table
echo -e "LOG: creating metadata table" >> ${repRID}.aggrQC.log
- echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in\tRaw-Reads\tAssigned-Read:\tMedia-Length\tMedian-TIN" > metadata.tsv
+ echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in\tRaw Reads\tAssigned Reads\tMedian Read Length\tMedian TIN" > metadata.tsv
echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t-\t'${readLengthM}'\t-" >> metadata.tsv
echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
echo -e "Measured\t-\t${endsManual}\t-\t-\t'${rawReadsI}'\t'${assignedReadsI}'\t'${readLengthI}'\t'${tinMedI}'" >> metadata.tsv
@@ -1045,4 +1045,4 @@ process aggrQC {
echo -e "LOG: running multiqc" >> ${repRID}.aggrQC.log
multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
"""
-}
\ No newline at end of file
+}
--
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