From 88280ca1e495f0e1f0ec014635799c784f1f0ca3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 2 Jun 2023 13:48:38 +0200
Subject: [PATCH 1/2] revert samtools_sort to no memory assignement

---
 modules.json                          | 6 +++---
 modules/nf-core/samtools/sort/main.nf | 2 --
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/modules.json b/modules.json
index b2fe8ca92..030893337 100644
--- a/modules.json
+++ b/modules.json
@@ -161,7 +161,7 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
@@ -252,9 +252,9 @@
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": [
-                            "bam_dedup_stats_samtools_umitools",
                             "bam_markduplicates_picard",
-                            "bam_sort_stats_samtools"
+                            "bam_sort_stats_samtools",
+                            "bam_dedup_stats_samtools_umitools"
                         ]
                     },
                     "bedgraph_bedclip_bedgraphtobigwig": {
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 1e5181d41..2b7753fd8 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -21,13 +21,11 @@ process SAMTOOLS_SORT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def sort_memory = (task.memory.mega/task.cpus).intValue()
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools sort \\
         $args \\
         -@ $task.cpus \\
-        -m ${sort_memory}M \\
         -o ${prefix}.bam \\
         -T $prefix \\
         $bam

From d286eb3e971e3ae36e4ca6991f339550048f8cfa Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 2 Jun 2023 13:49:52 +0200
Subject: [PATCH 2/2] update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dafad351a..daae6c447 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,6 +25,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1016](https://github.com/nf-core/rnaseq/pull/1016) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #1025](https://github.com/nf-core/fetchngs/pull/1025) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
 - [PR #1038](https://github.com/nf-core/rnaseq/pull/1038) - Updated error log for count values when supplying `--additional_fasta`
+- [PR #1042](https://github.com/nf-core/rnaseq/pull/1042) - revert samtools_sort modules to no memory assignement
 
 ### Parameters