Add exit code 1 for umicollapse

nf-core · Apr 3, 2024 · 98b67ef · 98b67ef
1 parent 6f4b327
commit 98b67ef
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -142,6 +142,8 @@ process {
     withName: '.*:UMICOLLAPSE_FASTQ' {
         ext.args = { meta.single_end ? "--algo ${params.umitools_method} --two-pass" : "--method ${params.umitools_method} --two-pass --paired --remove-unpaired --remove-chimeric" }
         ext.prefix = { "${meta.id}.umi_dedup.sorted" }
+        errorStrategy = { task.exitStatus in (1) ? 'ignore' : 'retry' }
+
         publishDir = [
             path: { "${params.outdir}/umi_dedup/bam_deduplicated" },
             mode: params.publish_dir_mode,