From 8f50b748ab0d07d34e00cb81c658ef9ce8263043 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 11:35:52 -0600
Subject: [PATCH] Fix seqwho tsv output for multiqc
---
rna-seq.nf | 6 +++---
workflow/conf/multiqc_config.yaml | 6 ++----
2 files changed, 5 insertions(+), 7 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 78d24fa..f4f19d3 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -919,11 +919,11 @@ process seqwho {
fi
# save seqwho multiqc report
- echo -e "Read\tSeq Type\tSpecies\tConfidence\tSeq Type Confidence\tSeq Type Consensus\tSpecies Confidence" > seqwhoInfer.tsv
- echo -e "Read 1\t\${seqtypeR1}\t\${speciesR1}\t\${confidenceR1}\${seqtypeConfidenceR1}\t\${consensus}\t\${speciesConfidenceR1}" >> seqwhoInfer.tsv
+ echo -e "Read\tSeq Type\tSpecies\tSeq Type Confidence\tSeq Type Consensus\tSpecies Confidence" > seqwhoInfer.tsv
+ echo -e "Read 1\t\${seqtypeR1}\t\${speciesR1}\t\${seqtypeConfidenceR1}\t\${consensus}\t\${speciesConfidenceR1}" >> seqwhoInfer.tsv
if [ "${ends}" == "pe" ]
then
- echo -e "Read 2\t\${seqtypeR2}\t\${speciesR2}\t\${confidenceR2}\${seqtypeConfidenceR2}\t\${consensus}\t\${speciesConfidenceR2}" >> seqwhoInfer.tsv
+ echo -e "Read 2\t\${seqtypeR2}\t\${speciesR2}\t\t\${seqtypeConfidenceR2}\t\${consensus}\t\${speciesConfidenceR2}" >> seqwhoInfer.tsv
fi
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index fdcdcca..ae9e195 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -182,14 +182,12 @@ custom_data:
description: 'Inferred Sequence Type'
Species:
description: 'Inferred Species'
- Confidence:
- description: 'Call confidence'
Seq Type Confidence:
- description: 'Seqence type call confidence (1=high, 0=low)'
+ description: 'Seqence type call confidence'
Seq Type Consensus:
description: 'Low confidence sequence type call sampling inference consensus'
Species Confidence:
- description: 'Species call confidence (1=high, 0=low)'
+ description: 'Species call confidence'
sp:
run:
--
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