From a7f9d9dd1e5842de6cf38557ab2f6330bf5ffa8c Mon Sep 17 00:00:00 2001
From: jeantristanb <jeantristanb@free.fr>
Date: Tue, 19 Mar 2024 10:35:28 +0200
Subject: [PATCH] add strmem function and error in regenie

---
 assoc/main.nf | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/assoc/main.nf b/assoc/main.nf
index 3ac6194..bc81790 100755
--- a/assoc/main.nf
+++ b/assoc/main.nf
@@ -18,6 +18,12 @@
  *
  */
 
+def strmem(val){
+ return val as nextflow.util.MemoryUnit
+}
+
+
+
 //---- General definitions --------------------------------------------------//
 
 import java.nio.file.Paths;
@@ -2190,12 +2196,13 @@ if(params.regenie==1){
      path(rsrel) from filers_matrel_regenie
      tuple path(bed), path(bim), path(fam) from ch_regenie_assoc
    each pheno from pheno_cols_ch_regenie
+   errorStrategy { task.exitStatus == 1 ; return 'ignore' }
    publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.cmd"
    publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.list"
    publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.loco"
    publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.log"
    output : 
-    tuple val(our_pheno), path("$phef"),path("${out}_pred.list"), path("${out}_1.loco"),path(bed), path(bim), path(fam)  into ch_regenie_pheno
+    tuple val(our_pheno), path("$phef"),path("${out}_pred.list"), path("${out}_1.loco"),path(bed), path(bim), path(fam),  optional :true into ch_regenie_pheno
     path("${out}.log")
     path("*regenie_step1.cmd")
    script :