ignore extract taxa fails with exit code 2

artic-network · Jun 21, 2023 · 0503fd0 · 0503fd0
1 parent 9ff72e7
commit 0503fd0
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git 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
@@ -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"
 }