stop using System.exit, which is deprecated by nextflow

PGScatalog · Aug 6, 2024 · 5d1b07c · 5d1b07c
1 parent 125d2f0
commit 5d1b07c
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Showing 4 changed files with 4 additions and 8 deletions.
diff --git a/subworkflows/local/ancestry/ancestry_project.nf b/subworkflows/local/ancestry/ancestry_project.nf
@@ -273,7 +273,6 @@ workflow ANCESTRY_PROJECT {
 
 def projection_error(boolean fail) {
     if (fail) {
-        log.error "ERROR: Projection subworkflow failed"
-        System.exit(1)
+        error "ERROR: Projection subworkflow failed"
     }
 }
diff --git a/subworkflows/local/apply_score.nf b/subworkflows/local/apply_score.nf
@@ -138,8 +138,7 @@ workflow APPLY_SCORE {
 
 def aggregate_error(boolean fail) {
     if (fail) {
-        log.error "ERROR: No scores calculated!"
-        System.exit(1)
+        error "ERROR: No scores calculated!"
     }
 }
 

diff --git a/subworkflows/local/match.nf b/subworkflows/local/match.nf
@@ -73,7 +73,6 @@ workflow MATCH {
 
 def combine_error(boolean fail) {
     if (fail) {
-        log.error "ERROR: Matching subworkflow failed"
-        System.exit(1)
+        error "ERROR: Matching subworkflow failed"
     }
 }
diff --git a/subworkflows/local/report.nf b/subworkflows/local/report.nf
@@ -103,7 +103,6 @@ def annotate_sampleset(it) {
 
 def report_error(boolean fail) {
     if (fail) {
-        log.error "ERROR: No results report written!"
-        System.exit(1)
+        error "ERROR: No results report written!"
     }
 }