From be4bafc9bf3db6bd5bb271187bda6fe2c43f04bb Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 6 Aug 2020 09:38:17 -0500
Subject: [PATCH] Add quotes to multiqc tables
---
workflow/conf/multiqc_config.yaml | 24 ++++++++++++------------
workflow/rna-seq.nf | 8 ++++----
2 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index 99a861c..5d57d09 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -64,9 +64,9 @@ custom_data:
pconfig:
id: 'rid'
headers:
- Replicate RID
- Experiment RID
- Study RID
+ 'Replicate RID:'
+ 'Experiment RID:'
+ 'Study RID:'
meta:
file_format: 'tsv'
section_name: 'Metadata'
@@ -75,15 +75,15 @@ custom_data:
pconfig:
id: 'meta'
headers:
- Source
- Species
- Ends
- Stranded
- Spike-in
- Raw Reads
- Assigned Reads
- Median Read Length
- Median TIN
+ 'Source:'
+ 'Species:'
+ 'Ends:'
+ 'Stranded:'
+ 'Spike-in:'
+ 'Raw Reads:'
+ 'Assigned Reads:'
+ 'Median Read Length:'
+ 'Median TIN:'
file_format: 'tsv'
section_name: 'TIN'
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 7621289..f73e4ca 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1024,15 +1024,15 @@ process aggrQC {
# make RID table
echo -e "LOG: creating RID table" >> ${repRID}.aggrQC.log
- echo -e "Replicate RID\tExperiment RID\tStudy RID" > rid.tsv
+ echo -e "Replicate RID:\tExperiment RID:\tStudy RID:" > rid.tsv
echo -e "${repRID}\t${expRID}\t${studyRID}" >> rid.tsv
# make metadata table
echo -e "LOG: creating metadata table" >> ${repRID}.aggrQC.log
- echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in\tRaw Reads\tAssigned Reads\tMedian Read Length\tMedian TIN" > metadata.tsv
- echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t-\t${readLengthM}\t-" >> metadata.tsv
+ echo -e "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
+ echo -e "Measured\t-\t${endsManual}\t-\t-\t'${rawReadsI}'\t'${assignedReadsI}'\t'${readLengthI}'\t'${tinMedI}'" >> metadata.tsv
# remove inner distance report if it is empty (SE repRID)
echo -e "LOG: removing dummy inner distance file" >> ${repRID}.aggrQC.log
--
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