From 13bedeb6f42591eb73a149d563855423daffe901 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 5 Jan 2021 15:42:01 -0600
Subject: [PATCH] Fix parse
---
workflow/rna-seq.nf | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 35627ec..082aa09 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -290,6 +290,7 @@ process parseMetadata {
path experimentSettings, stageAs: "ExperimentSettings.csv" from experimentSettingsMeta
path experiment from experimentMeta
path (fastq) from fastqs_parseMetadata
+ val fastqCount
output:
path "design.csv" into metadata_fl
@@ -375,13 +376,15 @@ process parseMetadata {
fastqReadError_details=""
if [ "\${endsMeta}" == "pe" ]
then
- r1Count=\$(echo \$(zcat ${fastq[0]} | wc -l)/4 | bc)
- r2Count=\$(echo \$(zcat ${fastq[1]} | wc -l)/4 | bc)
- if [ \${r1Count} -ne \${r2Count} ]
+ r1Count=\$(zcat ${fastq[0]} | wc -l)
+ r2Count=\$(zcat ${fastq[1]} | wc -l)
+ if [ "\${r1Count}" -ne "\${r2Count}" ]
then
fastqReadError=true
fastqReadError_details="Number of reads do not match for R1 or R2, there may be a trunkation or mismatch of fastq files"
fi
+ fi
+
# save design file
echo -e "\${endsMeta},\${endsRaw},\${endsManual},\${stranded},\${spike},\${species},\${readLength},\${exp},\${study}" > design.csv
--
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