Ignore trim_galore exit 255

artic-network · Oct 17, 2024 · 71e3e7d · 71e3e7d
1 parent 4bfa36c
commit 71e3e7d
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diff --git a/modules/illumina.nf b/modules/illumina.nf
@@ -33,6 +33,8 @@ process readTrimming {
 
     conda 'bioconda::trim-galore=0.6.10'
 
+    errorStrategy {task.exitStatus == 255 ? "ignore" : "terminate"}
+
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: '*_val_{1,2}.fq.gz', mode: 'copy'
 
     input:

diff --git a/nextflow.config b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
   description = 'Epi2me compatible Nextflow pipeline for processing ARTIC tiling amplicon Illumina sequencing reads from monkeypox virus (MPXV) samples.'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version = '1.4.2'
+  version = '1.4.3'
   defaultBranch = 'main'
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -33,6 +33,8 @@ process readTrimming { @@
         conda 'bioconda::trim-galore=0.6.10'
+        errorStrategy {task.exitStatus == 255 ? "ignore" : "terminate"}
         publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: '*_val_{1,2}.fq.gz', mode: 'copy'
         input:
@@ Expand Down @@