diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a130e6dcb22212768d49f5dbd30de37bb489cc96..eb2aca53ab1f6f569b546cb5ae3561c532ab9f15 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,65 +42,65 @@ collect:
       derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
       derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${derivaImg}-${derivaVar}.sif)
-      singularity run ${img} deriva-download-cli --version > version_deriva.txt
-      singularity run ${img} bdbag --version > version_bdbag.txt
+      singularity run "${img}" deriva-download-cli --version > version_deriva.txt
+      singularity run "${img}" bdbag --version > version_bdbag.txt
     - >
       pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1)
       pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
       img=$(${dir}${pythonImg}-${pythonVar}.sif)
-      singularity run ${img} python3 --version > version_python.txt
+      singularity run "${img}" python3 --version > version_python.txt
     - >
       fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
       fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${fastqcImg}-${fastqcVar}.sif)
-      singularity run ${img} fastqc --version > version_fastqc.txt
+      singularity run "${img}" fastqc --version > version_fastqc.txt
     - >
       seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
       seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
       img=$(${dir}${seqwhoImg}-${seqwhoVar}.sif)
-      singularity run ${img} seqwho.py -h | grep -o Version.* > version_seqwho.txt
+      singularity run "${img}" seqwho.py -h | grep -o Version.* > version_seqwho.txt
     - >
       trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
       trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${trimgaloreImg}-${trimgaloreVar}.sif)
-      singularity run ${img} trim_galore --version > version_trimgalore.txt
+      singularity run "${img}" trim_galore --version > version_trimgalore.txt
     - >
       seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1)
       seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${seqtkImg}-${seqtkVar}.sif)
-      singularity run ${img} seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
+      singularity run "${img}" seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
     - >
       rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
       rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${rseqcImg}-${rseqcVar}.sif)
-      singularity run ${img} infer_experiment.py --version > version_rseqc.txt
+      singularity run "${img}" infer_experiment.py --version > version_rseqc.txt
     - >
       hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1)
       hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${hisatImg}-${hisatVar}.sif)
-      singularity run ${img} hisat2 --version > version_hisat2.txt
-      singularity run ${img} samtools --version > version_samtools.txt
+      singularity run "${img}" hisat2 --version > version_hisat2.txt
+      singularity run "${img}" samtools --version > version_samtools.txt
     - >
       picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1)
       picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${picardImg}-${picardVar}.sif)
-      singularity run ${img} java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
+      singularity run "${img}" java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
     - >
       subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
       subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${subreadImg}-${subreadVar}.sif)
-      singularity run ${img} featureCounts -v &> version_featurecounts.txt
-      singularity run ${img} R --version > version_r.txt
+      singularity run "${img}" featureCounts -v &> version_featurecounts.txt
+      singularity run "${img}" R --version > version_r.txt
     - >
       deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1)
       deeptoolsVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${deeptoolsImg}-${deeptoolsVar}.sif)
-      singularity run ${img} deeptools --version > version_deeptools.txt
+      singularity run "${img}" deeptools --version > version_deeptools.txt
     - >
       multiqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f1)
       multiqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f2)
       img=$(echo ${dir}${multiqcImg}-${multiqcVar}.sif)
-      singularity run ${img} multiqc --version > version_multiqc.txt
+      singularity run "${img}" multiqc --version > version_multiqc.txt
   artifacts:
     name: "$CI_JOB_NAME"
     when: always