From 6bf99653043233ae0dd2c46ae05f5d268132e9e6 Mon Sep 17 00:00:00 2001
From: mcmero <7799828+mcmero@users.noreply.github.com>
Date: Fri, 24 May 2024 15:22:21 +1000
Subject: [PATCH] Save report and trace

Logging as previously configured will not work
with WEHI stornext read-only changes, so using
Nextflow execution reports for data provenance
instead.
---
 logger.config   | 19 -------------------
 nextflow.config | 10 ++++++++++
 2 files changed, 10 insertions(+), 19 deletions(-)
 delete mode 100644 logger.config

diff --git a/logger.config b/logger.config
deleted file mode 100644
index d1d8a3b..0000000
--- a/logger.config
+++ /dev/null
@@ -1,19 +0,0 @@
-process.afterScript = {
-    logMainDir = "${params.outdir}/log"
-    logMainDir = workflow.launchDir.resolve(logMainDir).toString()
-
-    // Build log directory path based on task name
-    logSubDir = task.name.replace(" (null)", "").replace(" ", "/").replaceAll(" ", "_").replaceAll("[()]", "")
-    logDir = logMainDir + "/" + logSubDir
-
-    // Define command to copy log files 
-    cpLogCmd = "mkdir -p ${logDir}; cp -a nxf_log.tar.gz ${logDir}; "
-
-    // Assemble final command
-    cmd =  "ls -alR > .command.ls; "
-    cmd += "mkdir nxf_log; "
-    cmd += "for file in .command.*; do cp -a \${file} nxf_log/\${file#.}.txt; done; "
-    cmd += "tar -czf nxf_log.tar.gz nxf_log;"
-    cmd += cpLogCmd
-    cmd
-}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 496653f..98786d0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -103,3 +103,13 @@ profiles {
         includeConfig 'logger.config'
     }
 }
+
+def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+report {
+    enabled = true
+    file    = "${params.outdir}/log/execution_report_${trace_timestamp}.html"
+}
+trace {
+    enabled = true
+    file    = "${params.outdir}/log/execution_trace_${trace_timestamp}.txt"
+}