From 072003d4d971d146a6cd671768cebf5ff0c566f2 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 16 Jul 2021 13:26:16 -0500
Subject: [PATCH] Fix caps.
---
rna-seq.nf | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 305106d..b273f86 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -812,7 +812,7 @@ process seqwho {
echo -e "LOG: concordant species inference: \${speciesInfer}" >> ${repRID}.seqwho.log
else
speciesErrorSeqwho=true
- speciesErrorSeqwho_details="**inferred species does not match for R1 and R2:** inferred R1 = \${speciesR1} and inferred R2 = \${speciesR2}"
+ speciesErrorSeqwho_details="**Inferred species does not match for R1 and R2:** Inferred R1 = \${speciesR1} and inferred R2 = \${speciesR2}"
echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
fi
@@ -822,8 +822,8 @@ process seqwho {
echo -e "LOG: high confidence species inference detected" >> ${repRID}.seqwho.log
else
speciesErrorSeqwho=true
- speciesErrorSeqwho_details=\$(echo "**inferred species confidence is low:**\\n")
- speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|inferred species confidence|\\n")
+ speciesErrorSeqwho_details=\$(echo "**Inferred species confidence is low:**\\n")
+ speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Inferred species confidence|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|:--|:--:|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 1|\${speciesConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
@@ -846,12 +846,12 @@ process seqwho {
echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
else
seqtypeError=true
- seqtypeError_details="**inferred sequencing type is not mRNA-seq:** inferred = \${seqtypeR1}"
+ seqtypeError_details="**Inferred sequencing type is not mRNA-seq:** Inferred = \${seqtypeR1}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
else
seqtypeError=true
- seqtypeError_details="**inferred sequencing type does not match for R1 and R2:** inferred R1 = \${seqtypeR1} and inferred R2 = \${seqtypeR2}"
+ seqtypeError_details="**Inferred sequencing type does not match for R1 and R2:** Inferred R1 = \${seqtypeR1} and inferred R2 = \${seqtypeR2}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
consensus="-"
@@ -901,8 +901,8 @@ process seqwho {
if [ \${consensus} == false ]
then
seqtypeError=true
- seqtypeError_details=\$(echo "**inferred sequence-type confidence is low:**\\n")
- seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|inferred seq type|inferred seq type confidence|\\n")
+ seqtypeError_details=\$(echo "**Inferred sequence-type confidence is low:**\\n")
+ seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|Inferred seq type|Inferred seq type confidence|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
--
GitLab