From e0487109f2ffb14c393c784646571aacbf54a2fa Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 31 Jul 2023 13:48:03 +0200
Subject: [PATCH 1/2] Apply easy module updates

Some other module updates are available, but those will require changes to the pipeline code.
---
 modules.json                              |  6 +++---
 modules/nf-core/fastqc/main.nf            |  6 +++++-
 modules/nf-core/samtools/flagstat/main.nf | 11 +++++++++++
 modules/nf-core/samtools/sort/main.nf     |  2 --
 4 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/modules.json b/modules.json
index 2b51dee0..318b4e71 100644
--- a/modules.json
+++ b/modules.json
@@ -62,7 +62,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
                         "installed_by": ["modules"]
                     },
                     "methyldackel/extract": {
@@ -107,7 +107,7 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
@@ -117,7 +117,7 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 07d5e433..249f9064 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,11 @@ process FASTQC {
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
-    fastqc $args --threads $task.cpus $renamed_files
+
+    fastqc \\
+        $args \\
+        --threads $task.cpus \\
+        $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index eb7e72fc..b75707ec 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.flagstat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 1e5181d4..2b7753fd 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 ace1a391c9976a16ec4decebb412cf4a8dace62c Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 31 Jul 2023 13:50:58 +0200
Subject: [PATCH 2/2] Changelog

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9ea33412..0cb85852 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,9 @@
 
 ### Pipeline Updates
 
+- Updated nf-core modules for FastQC, samtools sort, samtools flagstat
+  - Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81)
+
 ### Bug fixes & refactoring
 
 ## [v2.4.0](https://github.com/nf-core/methylseq/releases/tag/2.4.0) - 2023-06-02