From 41f6e91a74ea77494de24489b2eb6fbfbdbcd247 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 19 Jan 2021 20:08:56 -0600
Subject: [PATCH] Handle blank endness better
---
CHANGELOG.md | 1 +
workflow/rna-seq.nf | 6 ++----
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e0882b..b285b5d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
* Add error output for no fastq's
* Update input bag export config to only fetch fastq's that match *[_.]R[1-2].fastq.gz naming convention
* Remove check for multiple fastq check in parse metadata (redundant and no longer valid)
+* Handle blank submitted endness better
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 4b0056b..caba704 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -337,12 +337,10 @@ process parseMetadata {
elif [ "\${endsRaw}" == "Paired End" ]
then
endsMeta="pe"
- else
- endsMeta=\${endsRaw}
- fi
- if [ "\${endsRaw}" == "" ]
+ elseif [ "\${endsRaw}" == "nan" ]
then
endsRaw="_No value_"
+ endsMeta="NA"
fi
# ganually get endness
--
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