From 5d1b07c58aaaad313ec313750f66be4119b63546 Mon Sep 17 00:00:00 2001 From: Benjamin Wingfield Date: Tue, 6 Aug 2024 15:46:21 +0100 Subject: [PATCH] stop using System.exit, which is deprecated by nextflow --- subworkflows/local/ancestry/ancestry_project.nf | 3 +-- subworkflows/local/apply_score.nf | 3 +-- subworkflows/local/match.nf | 3 +-- subworkflows/local/report.nf | 3 +-- 4 files changed, 4 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/ancestry/ancestry_project.nf b/subworkflows/local/ancestry/ancestry_project.nf index f8b09ad5..69f45cbe 100644 --- 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 index 00a6fbac..a56f3fbc 100644 --- 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 index f1c880c0..8b8ebae6 100644 --- 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 index c1fe7953..bbbd1ea6 100644 --- 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!" } }