From 0bba02cda9aae684df7db445794ae28a83fb282a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 13 Jun 2023 17:15:52 +0200
Subject: [PATCH] remove params.tracedir

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ac02ed465f..f59b5d76b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ Vuoinesluobbalah is a lake close to Bierikjávrre.
 - [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName.
 - [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094)
 - [#1100](https://github.com/nf-core/sarek/pull/1100) - Remove duplicate index with deepvariant when no_intervals [#1069](https://github.com/nf-core/sarek/pull/1069)
+- [#1105](https://github.com/nf-core/sarek/pull/1105) - Remove `params.tracedir`
 
 ## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure
 
diff --git a/nextflow.config b/nextflow.config
index 4941d3f6ad..2a8432ccf0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -99,7 +99,6 @@ params {
 
     // Boilerplate options
     outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
@@ -302,19 +301,19 @@ singularity.registry = 'quay.io'
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${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/nextflow_schema.json b/nextflow_schema.json
index fa71399258..05e5a83c4f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -959,13 +959,6 @@
                     "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",