From f39ef5bf289a148f961370712e27ad5e7bb3ffa0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Mar 2024 10:17:55 +0100 Subject: [PATCH 1/2] fix annoying PRESEQ failure for methylseq --- modules/nf-core/preseq/lcextrap/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index ebbf215f083..788dd507781 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -21,6 +21,7 @@ process PRESEQ_LCEXTRAP { script: def args = task.ext.args ?: '' + args = task.attempt > 1 ? args.join(' -defects') : args def prefix = task.ext.prefix ?: "${meta.id}" def paired_end = meta.single_end ? '' : '-pe' """ From 20583ca03f976e36c67a2befcc5a8335b754a988 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 11 Mar 2024 10:36:43 +0100 Subject: [PATCH 2/2] Update modules/nf-core/preseq/lcextrap/main.nf Co-authored-by: Phil Ewels --- modules/nf-core/preseq/lcextrap/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 788dd507781..0f8a1e9ec16 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -21,7 +21,7 @@ process PRESEQ_LCEXTRAP { script: def args = task.ext.args ?: '' - args = task.attempt > 1 ? args.join(' -defects') : 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' """