diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..5c40886496d66243c75fa01bd6b4c5f54e45529c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,8 @@
+work/
+singularity/
+results/
+.nextflow/
+.nextflow*
+dataset/
+OFNOTE.txt
+dev/
diff --git a/README.md b/README.md
index 846fb353ecfdbc1a0cb7b5cfb18006b21eb5576c..e612e0b14f223a6238723e0819034e8a8ec87271 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@
 ### 1. Prerequisite
 
 Installation of:<br />
-[nextflow DSL2](https://gael-millot.github.io/protocols/docs/Protocol%20152-rev0%20DSL2.html#_Toc159933761)<br />
+[nextflow DSL1](https://gael-millot.github.io/protocols/docs/Protocol%20152-rev0%20DSL2.html#_Toc159933761)<br />
 [Graphviz](https://www.graphviz.org/download/), `sudo apt install graphviz` for Linux ubuntu<br />
 [Apptainer](https://gael-millot.github.io/protocols/docs/Protocol%20135-rev0%20APPTAINER.html#_Toc160091693)<br />
 
diff --git a/main - Copy.nf b/main - Copy.nf
deleted file mode 100644
index b6579baa59ba249ea6ef4b527795d8007365dd8e..0000000000000000000000000000000000000000
--- a/main - Copy.nf	
+++ /dev/null
@@ -1,53 +0,0 @@
-
-process columnSorting {
-    label 'bash' // see the withLabel: bash in the nextflow config file 
-    publishDir "${out_path}", mode: 'copy', overwrite: false
-    cache 'false'
-
-    //no channel input here for the vcf, because I do not transform it
-    input:
-    file vcf_gz from vcf_ch3
-    val header_line_nb from header_line_nb_ch
-
-
-    output:
-    file "tempo.gz"
-    // file "tempo.gz" to have the file in the output result file
-
-    script:
-    """
-    zcat ${vcf_gz} | awk -v line=${header_line_nb} -v aff="$affected_patients_col_nb" -v unaff="$unaffected_patients_col_nb" '
-        BEGIN{
-            FS="\\t"
-            split(aff, array1, " ") # aff="10 12 14" and is added into the array1 array such that index 1 points to 10, index 2 to 12 and index 3 to 14
-            for(i in array1){
-                aff_arr[array1[i]]++ # a new aff_arr array is created such that the first index is 10 and points to 1, the second is 12 and points to 2, etc.
-            }
-            split(unaff, array2, " ")
-            for(i in array2){
-                unaff_arr[array2[i]]++
-            }
-        }{
-        if(NR < line){
-            print \$0
-        }else{
-            OFS=""
-            ORS=""
-            for(i=1;i<=NF;i++){
-                if( ! (i in aff_arr) && ! ( i in unff_arr)){ # warning: ! is only for the next (), not after. In addition, the in operator on arrays checks the array index. Thus, creating aff_arr was the simpliest way to have i in "12 14 16" 
-                    print \$i"\\t"
-                }
-            }
-            for(i in array1){
-                print \$array1[i]"\\t"
-            }
-            for(i in array2){
-                print \$array2[i]"\\t"
-            }
-            print "\\n"
-        }
-    }' | gzip > tempo.gz
-    """
-    // warning: ${in_path}/${sample_name} instead of ${vcf_gz} does not work, because the file used is not here anymore (do not use path in nextflow)
-}
-
diff --git a/main.nf b/main.nf
index d2bce4aad00af5b80e68e9ce9595f04dd1ba84d9..74b0cc595aa48dfdfe4c19abffed5ad88860748a 100644
--- a/main.nf
+++ b/main.nf
@@ -1,3 +1,4 @@
+nextflow.enable.dsl=1
 /*
 #########################################################################
 ##                                                                     ##
@@ -65,7 +66,7 @@ patient_name_ch = Channel.value(["affected_patients", "unaffected_patients"]) //
 if(system_exec == 'local' || system_exec == 'slurm'){
     def file_exists1 = in_path_test.exists()
     if( ! file_exists1){
-        error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID sample_path PARAMETER IN nextflow.config FILE: ${sample_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+        error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID in_path_test PARAMETER IN nextflow.config FILE: ${in_path_test}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
     }
     def file_exists2 = log_file.exists()
     if( ! file_exists2){
diff --git a/nextflow.config b/nextflow.config
index fb3a8c8d5b3e4d14512fa35271f6dfa6da06c471..d6a97eb1be23bb72e14fd28ae0426dc49ddb9269 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -35,7 +35,7 @@
 env {
     git_path="https://gitlab.pasteur.fr/Gael/08002_bourgeron/"
     //in_path="/pasteur/gaia/projets/p02/ghfc_wgs/Transfert/Dyslexia"
-    in_path="/mnt/share/Users/Gael/Documents/Git_projects/08002_bourgeron/dataset"
+    in_path="/mnt/c/Users/gmillot/Documents/Git_projects/nf_column_reorder/dataset"
     //sample_name="Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz"
     sample_name="test.vcf.gz" // Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
    //Warning: do not write the out_path now. See below. If written here, the one below is not considered"
@@ -153,7 +153,7 @@ dag {
 
 
 // define apptainer parameters
-apptainer {
+singulariry {
     enabled = true
     autoMounts = true // automatically mounts host paths in the executed container
     if(system_exec == 'slurm' || system_exec == 'slurm_local'){