From 7bcdead306b2542f67ed8e542d56fc231158d159 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 13 Aug 2020 12:13:27 -0500
Subject: [PATCH] Remove parallelization of trim_galore
---
.gitlab-ci.yml | 4 ++--
workflow/rna-seq.nf | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5d16e64..9a846f6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -65,8 +65,8 @@ getRef:
trimData:
stage: unit
script:
- - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se -j 4 ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
- - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe -j 4 ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
+ - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
+ - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
- readLengthSE=$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
- readLengthPE=$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
- pytest -m trimData
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 2c5e6fd..9a9b553 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -304,11 +304,11 @@ process trimData {
echo -e "LOG: trimming ${ends}" >> ${repRID}.trimData.log
if [ "${ends}" == "se" ]
then
- trim_galore --gzip -q 25 --length 35 --basename ${repRID} -j 4 ${fastq[0]}
+ trim_galore --gzip -q 25 --length 35 --basename ${repRID} ${fastq[0]}
readLength=\$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length(\$1)}' | sort -n | awk '{a[NR]=\$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
elif [ "${ends}" == "pe" ]
then
- trim_galore --gzip -q 25 --length 35 --paired --basename ${repRID} -j 4 ${fastq[0]} ${fastq[1]}
+ trim_galore --gzip -q 25 --length 35 --paired --basename ${repRID} ${fastq[0]} ${fastq[1]}
readLength=\$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length(\$1)}' | sort -n | awk '{a[NR]=\$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
fi
echo -e "LOG: trimmed" >> ${repRID}.trimData.log
--
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