diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf
index a8954311..0e5bfd7b 100644
--- a/modules/local/annotation/full_annotation/main.nf
+++ b/modules/local/annotation/full_annotation/main.nf
@@ -40,8 +40,8 @@ process ANNOTATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' )
         bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        busybox: \$(busybox | head -1)
         ucsc: $VERSION
     END_VERSIONS
     """
diff --git a/modules/local/ciriquant/filter/main.nf b/modules/local/ciriquant/filter/main.nf
index 38520091..017d8990 100644
--- a/modules/local/ciriquant/filter/main.nf
+++ b/modules/local/ciriquant/filter/main.nf
@@ -24,16 +24,16 @@ process CIRIQUANT_FILTER {
     def VERSION = '1.3.4'
     """
     grep -v "#" ${prefix}.gtf | awk '{print \$14}' | cut -d '.' -f1 > counts
-    grep -v "#" ${prefix}.gtf | awk -v OFS="\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp
+    grep -v "#" ${prefix}.gtf | awk -v OFS="\\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp
     paste ${prefix}.tmp counts > ${prefix}_unfilt.bed
 
     awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}_unfilt.bed > ${prefix}_filt.bed
     grep -v '^\$' ${prefix}_filt.bed > ${prefix}_ciriquant
 
-    awk -v OFS="\t" '{\$2-=1;print}' ${prefix}_ciriquant > ${prefix}_ciriquant.bed
+    awk -v OFS="\\t" '{\$2-=1;print}' ${prefix}_ciriquant > ${prefix}_ciriquant.bed
     rm ${prefix}.gtf
 
-    awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed
+    awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf
index 6718df4b..c92bb922 100644
--- a/modules/local/ciriquant/yml/main.nf
+++ b/modules/local/ciriquant/yml/main.nf
@@ -32,6 +32,6 @@ process CIRIQUANT_YML {
     SAMTOOLS=`which samtools`
 
     touch travis.yml
-    printf "name: ciriquant\ntools:\n  bwa: \$BWA\n  hisat2: \$HISAT2\n  stringtie: \$STRINGTIE\n  samtools: \$SAMTOOLS\n\nreference:\n  fasta: ${fasta_path}\n  gtf: ${gtf_path}\n  bwa_index: ${bwa_path}/${bwa_prefix}\n  hisat_index: ${hisat2_path}/${hisat2_prefix}" >> travis.yml
+    printf "name: ciriquant\\ntools:\\n  bwa: \$BWA\\n  hisat2: \$HISAT2\\n  stringtie: \$STRINGTIE\\n  samtools: \$SAMTOOLS\\n\\nreference:\\n  fasta: ${fasta_path}\\n  gtf: ${gtf_path}\\n  bwa_index: ${bwa_path}/${bwa_prefix}\\n  hisat_index: ${hisat2_path}/${hisat2_prefix}" >> travis.yml
     """
 }
diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf
index 07ff052e..f7b25149 100644
--- a/modules/local/stringtie/prepde/main.nf
+++ b/modules/local/stringtie/prepde/main.nf
@@ -19,7 +19,11 @@ process STRINGTIE_PREPDE {
 
     script:
     """
-    for file in \$(ls *.gtf); do sample_id=\${file%".transcripts.gtf"}; touch samples.txt; printf "\$sample_id\t\$file\n" >> samples.txt ; done
+    for file in \$(ls *.gtf); do 
+        sample_id=\${file%".transcripts.gtf"}
+        touch samples.txt
+        printf "\$sample_id\\t\$file\\n" >> samples.txt
+    done
 
     prepDE.py -i samples.txt
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f7b22160..9aefc770 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -48,7 +48,7 @@
                     "type": "string",
                     "fa_icon": "fas fa-wrench",
                     "description": "Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, circexplorer2, find_circ, circrna_finder, mapsplice, dcc, segemehl",
-                    "help_text": "Select one or a combination of circRNA quantification tools for the pipeline e.g:\n--tool 'circexplorer2, ciriquant, find_circ'\n\nN.B: Selecting more than one circRNA quantification tool will trigger the circRNA filtering parameter --tool_filter",
+                    "help_text": "Select one or a combination of circRNA quantification tools for the pipeline e.g:\n--tool 'circexplorer2,ciriquant,find_circ'\n\nN.B: Selecting more than one circRNA quantification tool will trigger the circRNA filtering parameter --tool_filter",
                     "default": "circexplorer2",
                     "pattern": "^((circexplorer2|circrna_finder|ciriquant|dcc|find_circ|mapsplice|segemehl)?,?)*[^,]+$"
                 },
@@ -58,7 +58,7 @@
                     "description": "Comma separated list of modules to run: 'circrna_discovery', 'mirna_prediction' & 'differential_expression'.",
                     "mandatory": "circrna_discovery",
                     "pattern": "^((circrna_discovery|mirna_prediction|differential_expression)?,?)*[^,]+$",
-                    "help_text": "The 'circrna_discovery' module is mandatory. After circRNA quantification, the user can select 'mirna_prediction', 'differential_expression' or both to deploy additional analyses e.g:\n--module 'circrna_discovery, mirna_prediction, differential_expression'\n",
+                    "help_text": "The 'circrna_discovery' module is mandatory. After circRNA quantification, the user can select 'mirna_prediction', 'differential_expression' or both to deploy additional analyses e.g:\n--module 'circrna_discovery,mirna_prediction,differential_expression'\n",
                     "default": "circrna_discovery"
                 },
                 "bsj_reads": {