From e0b3d4bd3d2b3494c7d3e82aad0212bfe1e8614f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 6 Aug 2020 11:48:41 -0500
Subject: [PATCH] Remove quotes and colons from multiqc custom tables
---
workflow/conf/multiqc_config.yaml | 24 ++++++++++++------------
workflow/rna-seq.nf | 4 ++--
2 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index 5d57d09..9cf4a9a 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-Length
+ Median-TIN
file_format: 'tsv'
section_name: 'TIN'
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index f73e4ca..f0a63c6 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1024,12 +1024,12 @@ 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" >> ${repRID}.aggrQC.log
- echo -e "Source\tSpecies:\tEnds:\tStranded:\tSpike-in:\tRaw Reads:\tAssigned Reads:\tMedian Read Length:\tMedian TIN:" > metadata.tsv
+ echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in\tRaw-Reads\tAssigned-Read:\tMedia-Length\tMedian-TIN" > metadata.tsv
echo -e "Submitter\t${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
--
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