From f798539f12d4640e3e255d36f24f4bced8aad0e0 Mon Sep 17 00:00:00 2001
From: gmillot <gael.millot@pasteur.fr>
Date: Tue, 3 Dec 2024 13:04:09 +0100
Subject: [PATCH] debuuged
---
.gitignore | 8 ++++++++
README.md | 2 +-
main - Copy.nf | 53 -------------------------------------------------
main.nf | 3 ++-
nextflow.config | 4 ++--
5 files changed, 13 insertions(+), 57 deletions(-)
create mode 100644 .gitignore
delete mode 100644 main - Copy.nf
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..5c40886
--- /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 846fb35..e612e0b 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 b6579ba..0000000
--- 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 d2bce4a..74b0cc5 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 fb3a8c8..d6a97eb 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'){
--
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