From db8c5a2880f1899b524ccb649051f304a2824e24 Mon Sep 17 00:00:00 2001
From: "Lataretu, Marie" <LataretuM@rki.de>
Date: Wed, 15 Apr 2026 11:36:25 +0200
Subject: [PATCH] ignore artic-medaka fails with exit status 20

- when no reads map to the reference, ARTIC medaka fails with a segfault while reading an empty VCF file (see vcfcheck.log in workdir)
- I would have liked to catch such samples before the ARTIC step, however Kraken2 classifies some reads as SC2, however no reads map in the end
---
 poreCov.nf                 | 2 +-
 workflows/process/artic.nf | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/poreCov.nf b/poreCov.nf
index 7fe30ca..4c02a64 100755
--- a/poreCov.nf
+++ b/poreCov.nf
@@ -313,7 +313,7 @@ workflow {
 
             // rename barcodes based on --samples input.csv
                 if (params.samples) { fastq_input_ch = fastq_input_raw_ch.join(samples_input_ch).map { it -> tuple(it[2],it[1])} 
-                   fastq_input_raw_ch.join(samples_input_ch).ifEmpty{ exit 2, "Could not match barcode numbers from $params.samples to the read files, some typo?"} 
+                    fastq_input_raw_ch.join(samples_input_ch).ifEmpty{ exit 2, "Could not match barcode numbers from $params.samples to the read files, some typo?"} 
                 }
                 else if (!params.samples) { fastq_input_ch = fastq_input_raw_ch }
 
diff --git a/workflows/process/artic.nf b/workflows/process/artic.nf
index f8c871e..d5ff8eb 100755
--- a/workflows/process/artic.nf
+++ b/workflows/process/artic.nf
@@ -1,5 +1,6 @@
 process artic_medaka {
         label 'artic'
+        errorStrategy {task.exitStatus == 20 ? 'ignore' : 'retry'}
         publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "*.consensus.fasta"
         publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
         publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"
@@ -68,6 +69,7 @@ process artic_medaka {
 
 process artic_medaka_custom_bed {
         label 'artic'
+        errorStrategy {task.exitStatus == 20 ? 'ignore' : 'retry'}
         publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "*.consensus.fasta"
         publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
         publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"