Removed scripts from inputs and updated templates

structuralvariants/nextflow/modules/codex_filter.nf

 process CODEX_FILTER {
-  tag "codex filter"
+  tag { "codex filter" }
 
   input:
     path input
@@ -10,10 +10,10 @@ process CODEX_FILTER {
     val min_lratio
 
   output:
-    path "*.bed", emit: output
+    path "*.bed"
 
   script:
   """
-  sh $script $input $samples $min_len $max_len $min_lratio
+  sh $projectDir/templates/codex_filter.sh $input $samples $min_len $max_len $min_lratio
   """
 }
\ No newline at end of file

structuralvariants/nextflow/modules/exomedepth_filter.nf

 process EXOMEDEPTH_FILTER {
-  tag "exomedepth filter"
+  tag { "exomedepth filter" }
   
   input:
-    path script
     path input
     path samples
     val max_len
@@ -10,10 +9,10 @@ process EXOMEDEPTH_FILTER {
     val min_bf
 
   output:
-    path "*.bed", emit: output
+    path "*.bed"
 
   script:
   """
-  sh $script $input $sample $min_len $max_len $min_bf
+  sh $projectDir/templates/exomedepth_filter.sh $input $sample $min_len $max_len $min_bf
   """
 }
\ No newline at end of file

structuralvariants/nextflow/modules/manta_filter.nf

@@ -2,7 +2,6 @@ process MANTA_FILTER {
   tag { "manta filter" }
 
   input:
-    path script
     path input
     path samples
     val max_len
@@ -10,13 +9,13 @@ process MANTA_FILTER {
     val min_q
 
   output:
-    path "*", emit: output
+    path "*"
 
   script:
   """
   for i in $input
   do
-    sh $script \$i $samples $min_len $max_len $min_q
+    sh $projectDir/templates/manta_filter.sh \$i $samples $min_len $max_len $min_q
   done
   """
 }

structuralvariants/nextflow/modules/merge_all.nf

 process MERGE_ALL {
-  tag "merge all"
+  tag { "merge all" }
   container 'quay.io/biocontainers/bedtools:2.26.0gx--he513fc3_4'
 
   input:
     path input
-    path script
 
   output:
-    path "*.bed", emit: output
+    path "*.bed"
 
   script:
-  """
-  sh $script $input
-  """
+  template "merge_all.sh"
 }
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structuralvariants/nextflow/subworkflows/final_filtering.nf

@@ -14,11 +14,10 @@ include {
 workflow SUB_FINAL_FILTERING {
     take:
         cnv_results
-        merge_all_script
         
     main:
         UNION( cnv_results )
-        MERGE( UNION.out, merge_all_script )
+        MERGE( UNION.out )
 
     emit:
         output = MERGE.out

structuralvariants/nextflow/templates/merge_all.sh

 #!/bin/bash
-INPUT_FILE=$1
-OUTPUT_NAME=${INPUT_FILE/bed/sorted.merged.bed}
-OUTPUT_FILE=$(echo "$OUTPUT_NAME" | sed "s/.*\///")
+INPUT_FILE=$input
+OUTPUT_NAME=\${INPUT_FILE/bed/sorted.merged.bed}
+OUTPUT_FILE=\$(echo "\$OUTPUT_NAME" | sed "s/.*\\///")
 
-for i in $(cat $INPUT_FILE | sed -e "s/[[:space:]]\+/\t/g" | cut -f4 | sort -u)  # FIXME: remove sed -e "s/[[:space:]]\+/\t/g" try better solution
+for i in \$(cat \$INPUT_FILE | sed -e "s/[[:space:]]\\+/\\t/g" | cut -f4 | sort -u)
 do
   for j in "DEL" "DUP"
   do
-    grep $i $INPUT_FILE | grep $j | sed -e "s/[[:space:]]\+/\t/g" | bedtools sort | bedtools merge -c 6,7 -o collapse | awk -v sample=$i -v type=$j '{ \
-      print $1,$2,$3,sample,type,$4,$5}' OFS="\t"
-  done >> ${OUTPUT_FILE}
+    grep \$i \$INPUT_FILE | grep \$j | sed -e "s/[[:space:]]\\+/\\t/g" | bedtools sort | bedtools merge -c 6,7 -o collapse | awk -v sample=\$i -v type=\$j '{ \\
+      print \$1,\$2,\$3,sample,type,\$4,\$5}' OFS="\\t"
+  done >> \${OUTPUT_FILE}
 done
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