From b88c1916b4cca9d9298984e3fe2bffee1ca5f0fe Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Tue, 3 Jun 2025 13:33:29 +0200
Subject: [PATCH 1/2] fix output file name

---
 modules/reditools3.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/reditools3.nf b/modules/reditools3.nf
index 5bb7f8b..3964895 100644
--- a/modules/reditools3.nf
+++ b/modules/reditools3.nf
@@ -27,8 +27,9 @@ process reditools3 {
             // the reditools error message
             strand_orientation = meta.libtype
         }
+        base_name = bam.BaseName
 
         """
-        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file edit_table.txt
+        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file ${base_name}.site_edits_reditools3.txt
         """
 }

From d9a04b01db0ec568ee1da3d1b3e13aa31cffc52d Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Tue, 3 Jun 2025 13:56:45 +0200
Subject: [PATCH 2/2] emit log and set thread numbers for reditools3

---
 config/ressources/hpc.config   |  4 ++++
 config/ressources/local.config | 11 +++++++++++
 modules/reditools3.nf          |  5 +++--
 3 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/config/ressources/hpc.config b/config/ressources/hpc.config
index dbf1c65..68cbf9b 100644
--- a/config/ressources/hpc.config
+++ b/config/ressources/hpc.config
@@ -28,4 +28,8 @@ process {
         cpus = 8
         time = '4d'
     }
+    withName: 'reditools3' {
+        cpus = 6
+        time = '4d'
+    }
 }
diff --git a/config/ressources/local.config b/config/ressources/local.config
index 06e430c..80e1b4a 100644
--- a/config/ressources/local.config
+++ b/config/ressources/local.config
@@ -18,6 +18,11 @@ process {
         memory = "4G"
         time = '1d'
     }
+    withLabel: 'agat' {
+        cpus = 1
+        memory = "2G"
+        time = '1d'
+    }
     withLabel: 'hisat2_index' {
         cpus = 4
         time = '1h'
@@ -35,7 +40,13 @@ process {
         time = '1d'
     }
     withLabel: 'bamutil' {
+        cpus = 1
+        time = '1d'
+        memory="12G"
+    }    
+    withLabel: 'reditools3' {
         cpus = 2
         time = '1d'
+        memory="4G"
     }    
 }
diff --git a/modules/reditools3.nf b/modules/reditools3.nf
index 3964895..523aa6d 100644
--- a/modules/reditools3.nf
+++ b/modules/reditools3.nf
@@ -8,7 +8,8 @@ process reditools3 {
         path genome
 
     output:
-        tuple(val(meta), path("edit_table.txt"), emit: tuple_sample_serial_table)
+        tuple(val(meta), path("${base_name}.site_edits_reditools3.txt"), emit: tuple_sample_serial_table)
+        path("${base_name}.reditools3.log", emit: log)
 
     script:
         // Set the strand orientation parameter from the library type parameter
@@ -30,6 +31,6 @@ process reditools3 {
         base_name = bam.BaseName
 
         """
-        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file ${base_name}.site_edits_reditools3.txt
+        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file ${base_name}.site_edits_reditools3.txt --threads ${task.cpus} --verbose > ${base_name}.reditools3.log
         """
 }