From c17649edd838e464092e33efdca626b53f46ca22 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 2 May 2020 01:10:56 -0500
Subject: [PATCH] Fix floating point errors
---
workflow/rna-seq.nf | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 211ff06..a5f9eab 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -453,19 +453,22 @@ process inferMetadata {
hostname > ${repRID}.inferMetadata.err
ulimit -a >> ${repRID}.inferMetadata.err
- # collect alignment rates
+ # collect alignment rates (round down to integers)
align_ercc=\$(echo \$(grep "Overall alignment rate" ERCC.alignSampleSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%'))
+ align_ercc=\$(echo \${align_ercc%.*})
align_hu=\$(echo \$(grep "Overall alignment rate" GRCh.alignSampleSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%'))
+ align_hu=\$(echo \${align_hu%.*})
align_mo=\$(echo \$(grep "Overall alignment rate" GRCm.alignSampleSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%'))
-
+ align_mo=\$(echo \${align_mo%.*})
+
# determine spike-in
- if [ 1 -eq \$(echo \$(expr \${align_ercc} ">=" 0.1)) ]
+ if [ 1 -eq \$(echo \$(expr \${align_ercc} ">=" 10)) ]
then
spike="yes"
else
spike="no"
fi
- echo -e "LOG: Inference of strandedness results in: \${spike}" >> ${repRID}.inferMetadata.err
+ echo -e "LOG: Inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.err
# determine species
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 25)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 25)) ]
@@ -479,7 +482,7 @@ process inferMetadata {
bam="GRCm.sampled.sorted.bam"
bed="./GRCm/bed/genome.bed"
else
- echo "LOG: ERROR - Inference of species returns an ambiguous result" >> ${repRID}.inferMetadata.err
+ echo -e "LOG: ERROR - Inference of species returns an ambiguous result: hu=\${align_hu} mo=\${align_mo}" >> ${repRID}.inferMetadata.err
exit 1
fi
echo -e "LOG: Inference of species results in: \${species}" >> ${repRID}.inferMetadata.err
@@ -502,10 +505,10 @@ process inferMetadata {
percentF=`bash inferMeta.sh sef ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
percentR=`bash inferMeta.sh ser ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
fi
- if [ 1 -eq \$(echo \$(expr \${percentF} ">" 0.25)) ] && [ 1 -eq \$(echo \$(expr \${percentR} "<" 0.25)) ]
+ if [ 1 -eq \$(echo \$(expr \${percentF#.*} ">" 25)) ] && [ 1 -eq \$(echo \$(expr \${percentR#.*} "<" 25)) ]
then
stranded="forward"
- elif [ 1 -eq \$(echo \$(expr \${percentR} ">" 0.25)) ] && [ 1 -eq \$(echo \$(expr \${percentF} "<" 0.25)) ]
+ elif [ 1 -eq \$(echo \$(expr \${percentR#.*} ">" 25)) ] && [ 1 -eq \$(echo \$(expr \${percentF#.*} "<" 25)) ]
then
stranded="reverse"
--
GitLab