diff --git a/modules/extract_taxa.nf b/modules/extract_taxa.nf index dd6b434..3484984 100644 --- a/modules/extract_taxa.nf +++ b/modules/extract_taxa.nf @@ -11,6 +11,8 @@ process extract_paired_reads { label 'process_high' + errorStrategy {task.exitStatus == 2 ? 'ignore' : 'terminate'} + publishDir path: "${params.out_dir}/${unique_id}/reads_by_taxa", mode: 'copy' conda 'bioconda::biopython=1.78 bioconda::tabix=1.11' @@ -52,6 +54,8 @@ process extract_reads { label 'process_high' + errorStrategy {task.exitStatus == 2 ? 'ignore' : 'terminate'} + publishDir path: "${params.out_dir}/${unique_id}/reads_by_taxa", mode: 'copy' conda 'bioconda::biopython=1.78 bioconda::tabix=1.11' diff --git a/nextflow.config b/nextflow.config index 2766db6..b6980eb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -143,19 +143,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.tracedir}/execution_timeline_${params.unique_id}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.tracedir}/execution_report_${params.unique_id}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.tracedir}/execution_trace_${params.unique_id}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.tracedir}/pipeline_dag_${params.unique_id}.html" }