From b858a9d73e4f24e4e1f268cad7445cd46f3783f3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 28 Feb 2021 16:23:05 -0600
Subject: [PATCH] Disconnect confidence from species and seq type inference
---
rna-seq.nf | 69 +++++++++++++++++++++++++++++-------------------------
1 file changed, 37 insertions(+), 32 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index eb7e075..cb1e7f4 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -741,6 +741,11 @@ process seqwho {
seqtypeConfidenceR2="1"
fi
+ speciesErrorSeqwho=false
+ speciesErrorSeqwho_details=""
+ seqtypeError=false
+ seqtypeError_details=""
+
# convert numeric confidence to string
if [ \${speciesConfidenceR1} == "1" ]
then
@@ -768,46 +773,46 @@ process seqwho {
fi
echo -e "LOG: confidence converted to string" >> ${repRID}.seqwho.log
- # detect errors
- speciesErrorSeqwho=false
- speciesErrorSeqwho_details=""
- seqtypeError=false
- seqtypeError_details=""
- if [ "\${confidenceR1}" == "high" ] && [ "\${confidenceR2}" == "high" ]
+ # set species
+ if [ "\${speciesR1}" == "\${speciesR2}" ]
then
- echo -e "LOG: high confidence inference detected" >> ${repRID}.seqwho.log
- if [ "\${speciesR1}" == "\${speciesR2}" ]
+ speciesInfer=\${speciesR1}
+ if [ "\${speciesInfer}" == "human" ]
then
- speciesInfer=\${speciesR1}
- if [ "\${speciesInfer}" == "human" ]
- then
- speciesInfer="Homo sapiens"
- elif [ "\${speciesInfer}" == "mouse" ]
- then
- speciesInfer="Mus musculus"
- fi
- echo -e "LOG: concordant species inference: \${speciesInfer}" >> ${repRID}.seqwho.log
- else
- speciesErrorSeqwho=true
- speciesErrorSeqwho_details="**Infered species does not match for R1 and R2:** Infered R1 = \${speciesR1} and infered R2 = \${speciesR2}"
- echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
+ speciesInfer="Homo sapiens"
+ elif [ "\${speciesInfer}" == "mouse" ]
+ then
+ speciesInfer="Mus musculus"
fi
- if [ "\${seqtypeR1}" == "\${seqtypeR2}" ]
+ echo -e "LOG: concordant species inference: \${speciesInfer}" >> ${repRID}.seqwho.log
+ else
+ speciesErrorSeqwho=true
+ speciesErrorSeqwho_details="**Infered species does not match for R1 and R2:** Infered R1 = \${speciesR1} and infered R2 = \${speciesR2}"
+ echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
+ fi
+
+ # set seq type
+ if [ "\${seqtypeR1}" == "\${seqtypeR2}" ]
+ then
+ if [ "\${seqtypeR1}" == "rnaseq" ]
then
- if [ "\${seqtypeR1}" == "rnaseq" ]
- then
- seqtpeInfer="rnaseq"
- echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
- else
- seqtypeError=true
- seqtypeError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
- echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
- fi
+ seqtpeInfer="rnaseq"
+ echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
else
seqtypeError=true
- seqtypeError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
+ seqtypeError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
+ else
+ seqtypeError=true
+ seqtypeError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
+ echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
+ fi
+
+ # detect confidence errors
+ if [ "\${confidenceR1}" == "high" ] && [ "\${confidenceR2}" == "high" ]
+ then
+ echo -e "LOG: high confidence inference detected" >> ${repRID}.seqwho.log
else
speciesErrorSeqwho=true
speciesErrorSeqwho_details=\$(echo "**Infered species and or sequencing type confidence is low:**\\n")
--
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