diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5d16e644fdfec75c5974ce553746d8d0749a41d0..9a846f6e432738ec3ec1a11d9dcf4bca2d473ed1 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 2c5e6fdab5c910ae3c7337515fcd3abdd0bf79d9..9a9b553aaa01f19f28d47f620260c559336630ac 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