fix annoying PRESEQ failure for methylseq (#5091)

* fix annoying PRESEQ failure for methylseq * Update modules/nf-core/preseq/lcextrap/main.nf Co-authored-by: Phil Ewels <[email protected]> --------- Co-authored-by: Phil Ewels <[email protected]>
nf-core · Mar 11, 2024 · 4d178c5 · 4d178c5
1 parent 3236889
commit 4d178c5
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf
@@ -1,7 +1,7 @@
 process PRESEQ_LCEXTRAP {
     tag "$meta.id"
     label 'process_single'
-    label 'error_ignore'
+    label 'error_retry'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -21,6 +21,7 @@ process PRESEQ_LCEXTRAP {
 
     script:
     def args = task.ext.args ?: ''
+    args = task.attempt > 1 ? args.join(' -defects') : args  // Disable testing for defects
     def prefix = task.ext.prefix ?: "${meta.id}"
     def paired_end = meta.single_end ? '' : '-pe'
     """