From 94dcf28081a3d4474715ee534237bd87b40b8aa3 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Fri, 12 May 2023 11:35:03 -0400
Subject: [PATCH] remove-tracedir-param

---
 CHANGELOG.md                                   | 1 +
 nf_core/pipeline-template/nextflow.config      | 9 ++++-----
 nf_core/pipeline-template/nextflow_schema.json | 7 -------
 3 files changed, 5 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 945b56f15d..936de5b124 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - Added stub in modules template ([#2277])(https://github.com/nf-core/tools/pull/2277) [Contributed by @nvnieuwk]
 - Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286)
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
+- Remove `--tracedir` parameter
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2650572c93..8ce5d207e9 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -29,7 +29,6 @@ params {
 
     // Boilerplate options
     outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
@@ -205,19 +204,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 2743562d6c..ee7ac1932c 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -243,13 +243,6 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
-                "tracedir": {
-                    "type": "string",
-                    "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/pipeline_info",
-                    "fa_icon": "fas fa-cogs",
-                    "hidden": true
-                },
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",