From dc3db4a392761afed0e32b693cdb911ac0a183ed Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Fri, 10 May 2024 11:16:39 +1200
Subject: [PATCH] Increased time limit for REPEATMODELER_REPEATMODELER to 3
 days, REPEATMASKER to 2 days, EDTA_EDTA to 7 days, BRAKER3 to 7 days and
 EGGNOGMAPPER to 1 day

---
 .pre-commit-config.yaml |  4 +++-
 CHANGELOG.md            | 15 +++++++++++++++
 conf/base.config        | 15 +++++++++++++++
 nextflow.config         |  2 +-
 4 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bc85d76..b942ccd 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,8 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3eb74a0..0f49028 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,21 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 0.3.1 - [10-May-2024]
+
+### `Added`
+
+### `Fixed`
+
+1. Increased time limit for REPEATMODELER_REPEATMODELER to 3 days, REPEATMASKER to 2 days, EDTA_EDTA to 7 days, BRAKER3 to 7 days and EGGNOGMAPPER to 1 day
+
+### `Dependencies`
+
+1. NextFlow!>=23.04.4
+2. nf-validation=1.1.3
+
+### `Deprecated`
+
 ## 0.3.0 - [30-April-2024]
 
 ### `Added`
diff --git a/conf/base.config b/conf/base.config
index 3d30f22..464584c 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -66,6 +66,21 @@ process {
         memory              = { check_max( 200.GB * task.attempt, 'memory' ) }
     }
 
+    withName:REPEATMODELER_REPEATMODELER {
+        time                = { check_max( 3.days  * task.attempt, 'time'    ) }
+    }
+    withName:REPEATMASKER {
+        time                = { check_max( 2.days  * task.attempt, 'time'    ) }
+    }
+    withName:EDTA_EDTA {
+        time                = { check_max( 7.days  * task.attempt, 'time'    ) }
+    }
+    withName:BRAKER3 {
+        time                = { check_max( 7.days  * task.attempt, 'time'    ) }
+    }
+    withName:EGGNOGMAPPER {
+        time                = { check_max( 1.day  * task.attempt, 'time'    ) }
+    }
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
diff --git a/nextflow.config b/nextflow.config
index a9ae34a..eec5b1a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -58,7 +58,7 @@ manifest {
     description                 = """A NextFlow pipeline for pan-genome annotation"""
     mainScript                  = 'main.nf'
     nextflowVersion             = '!>=23.04.4'
-    version                     = '0.3.0'
+    version                     = '0.3.1'
     doi                         = ''
 }