From 71f498c2f1624f42e2180053b8f556fdb5e291ab Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 Jan 2021 22:34:06 -0600
Subject: [PATCH] Fix fail on ambiguous species
---
workflow/rna-seq.nf | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index af5dc1a..a4e2d0c 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -840,7 +840,7 @@ process inferMetadata {
fi
fi
- if !\${speciesError} && [ "${speciesForce}" = "" ]
+ if [ "\${speciesError" == false } && [ "${speciesForce}" = "" ]
then
# infer experimental setting from dedup bam
echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log
@@ -877,6 +877,9 @@ process inferMetadata {
stranded=""
spike=""
species=""
+ percentF=""
+ percentR=""
+ fail=""
fi
# write inferred metadata to file
--
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