From c17c1c2848266bc57ea10c59a96c2506101f1bc6 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 26 Feb 2024 09:29:22 +0000
Subject: [PATCH] Fix for Nextflow 24.01-edge: functions have to be defined in
 the main nextflow.config

https://github.com/nextflow-io/nextflow/issues/4722
---
 conf/base.config | 27 ---------------------------
 nextflow.config  | 27 +++++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index b89dd1c7..fae443f1 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -4,33 +4,6 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Increasing the number of CPUs often gives diminishing returns, so we increase it
-    following a logarithm curve. Example:
-        - 0 < value <= 1: start + step
-        - 1 < value <= 2: start + 2*step
-        - 2 < value <= 4: start + 3*step
-        - 4 < value <= 8: start + 4*step
-    In order to support re-runs, the step increase may be multiplied by the attempt
-    number prior to calling this function.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-// Modified logarithm function that doesn't return negative numbers
-def positive_log(value, base) {
-    if (value <= 1) {
-        return 0
-    } else {
-        return Math.log(value)/Math.log(base)
-    }
-}
-
-def log_increase_cpus(start, step, value, base) {
-    return check_max(start + step * (1 + Math.ceil(positive_log(value, base))), 'cpus')
-}
-
-
 process {
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
diff --git a/nextflow.config b/nextflow.config
index 529735e1..346afe1f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -260,3 +260,30 @@ def check_max(obj, type) {
         }
     }
 }
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Increasing the number of CPUs often gives diminishing returns, so we increase it
+    following a logarithm curve. Example:
+        - 0 < value <= 1: start + step
+        - 1 < value <= 2: start + 2*step
+        - 2 < value <= 4: start + 3*step
+        - 4 < value <= 8: start + 4*step
+    In order to support re-runs, the step increase may be multiplied by the attempt
+    number prior to calling this function.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+// Modified logarithm function that doesn't return negative numbers
+def positive_log(value, base) {
+    if (value <= 1) {
+        return 0
+    } else {
+        return Math.log(value)/Math.log(base)
+    }
+}
+
+def log_increase_cpus(start, step, value, base) {
+    return check_max(start + step * (1 + Math.ceil(positive_log(value, base))), 'cpus')
+}
+