From d215aa7124416fcbc8b972a7d9f61266e657d8d5 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Tue, 5 Dec 2023 10:19:13 +0000
Subject: [PATCH] The default memory settings work just fine and make things
 easier to manipulate

---
 modules/local/samtools_sormadup.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/local/samtools_sormadup.nf b/modules/local/samtools_sormadup.nf
index 8c1c530..c5a31ef 100644
--- a/modules/local/samtools_sormadup.nf
+++ b/modules/local/samtools_sormadup.nf
@@ -34,7 +34,6 @@ process SAMTOOLS_SORMADUP {
                     args.contains("--output-fmt cram") ? "cram" :
                     "bam"
     def reference = fasta ? "--reference ${fasta}" : ""
-    def sort_memory = ((task.memory.mega - 1024 * (1 + Math.ceil( meta.read_count / 100000000 )) * task.attempt)/task.cpus).intValue()
 
     """
     samtools collate \\
@@ -60,7 +59,6 @@ process SAMTOOLS_SORMADUP {
         -u \\
         -T ${prefix}.sort \\
         --threads $task.cpus \\
-        -m ${sort_memory}M \\
         - \\
     | \\
     samtools markdup \\