From c1e52e803a474abec74ae0f3e14f094485223253 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 5 Dec 2024 14:52:14 +0000
Subject: [PATCH] Change SETUP from 1 to 2.14

---
 .github/workflows/ci.yml         | 2 +-
 conf/base.config                 | 6 ------
 subworkflows/local/yaml_input.nf | 2 +-
 3 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c379c507..270afb6c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -36,7 +36,7 @@ jobs:
         uses: tj-actions/branch-names@v8
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2.14
         with:
           version: "${{ matrix.NXF_VER }}"
 
diff --git a/conf/base.config b/conf/base.config
index 38013674..1acb9d18 100755
--- a/conf/base.config
+++ b/conf/base.config
@@ -248,12 +248,6 @@ process {
         memory = { check_max( 100.GB    * task.attempt, 'memory'  ) }
     }
 
-    withName: FKUTILS_FKPROF {
-        cpus   = { check_max( 25        * task.attempt, 'cpus'    ) }
-        memory = { check_max( 1.GB     * ( reference.size() < 2e9 ? 50 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * Math.ceil( task.attempt * 1 ) ), 'memory'  ) }
-        time   = { check_max( 36.h      * task.attempt, 'time'    ) }
-    }
-
     //
     // GENERAL MODULE LIMITS
     //      Based on reports from SummaryStats
diff --git a/subworkflows/local/yaml_input.nf b/subworkflows/local/yaml_input.nf
index 2fe38c8c..566a8ddd 100755
--- a/subworkflows/local/yaml_input.nf
+++ b/subworkflows/local/yaml_input.nf
@@ -226,7 +226,7 @@ workflow YAML_INPUT {
     motif_len                        = selfcomp_data.motif_len
     mummer_chunk                     = selfcomp_data.mummer_chunk
 
-    synteny_paths                     = group.synteny
+    synteny_paths                    = group.synteny
 
     intron_size                      = intron_size.size