From 7a1b8519b1f0f476531c92e18f82b46e3aa53f03 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Mon, 12 Aug 2024 11:43:22 +0200
Subject: [PATCH 1/2] Update modules

---
 modules.json                                | 4 ++--
 modules/nf-core/cellranger/mkref/main.nf    | 4 ++++
 modules/nf-core/cellrangerarc/mkref/main.nf | 4 +++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/modules.json b/modules.json
index b92f66ef..aa186d98 100644
--- a/modules.json
+++ b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "cellranger/mkref": {
                         "branch": "master",
-                        "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
+                        "git_sha": "3549a361ce3401b6afd238a266389d78392a53f6",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkvdjref": {
@@ -42,7 +42,7 @@
                     },
                     "cellrangerarc/mkref": {
                         "branch": "master",
-                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "git_sha": "3549a361ce3401b6afd238a266389d78392a53f6",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
diff --git a/modules/nf-core/cellranger/mkref/main.nf b/modules/nf-core/cellranger/mkref/main.nf
index 4325c308..a719b778 100644
--- a/modules/nf-core/cellranger/mkref/main.nf
+++ b/modules/nf-core/cellranger/mkref/main.nf
@@ -22,6 +22,9 @@ process CELLRANGER_MKREF {
         error "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     def args = task.ext.args ?: ''
+    // --localcores is passed to the martian runtime and specifies the number of allocated jobs
+    // --nthreads is passed to the STAR index generation.
+    // see also https://github.com/nf-core/scrnaseq/issues/329
     """
     cellranger \\
         mkref \\
@@ -30,6 +33,7 @@ process CELLRANGER_MKREF {
         --genes=$gtf \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
+        --nthreads=${task.cpus} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/cellrangerarc/mkref/main.nf b/modules/nf-core/cellrangerarc/mkref/main.nf
index 079776ba..b030ae92 100644
--- a/modules/nf-core/cellrangerarc/mkref/main.nf
+++ b/modules/nf-core/cellrangerarc/mkref/main.nf
@@ -35,8 +35,9 @@ process CELLRANGERARC_MKREF {
         reference_name = "cellrangerarc_reference"
     }
 
+    // unlike cellranger mkref and spaceranger mkref, cellranger-arc mkref is not *yet* implemented in the
+    // 10x martian runtime. It is therefore not necessary to specify --localcores and --localmem
     """
-
     python3 <<CODE
 
     from os.path import exists
@@ -73,6 +74,7 @@ process CELLRANGERARC_MKREF {
     cellranger-arc \\
         mkref \\
         --config=config \\
+        --nthreads=${task.cpus} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

From ecf08e526f4cb2a49e8be24c69be46c4d23e0906 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Mon, 12 Aug 2024 11:46:09 +0200
Subject: [PATCH 2/2] Update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7c2c0edf..03bb0936 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
 - Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))
+- Fix resource specifications for `cellranger mkref`/`cellrangerarc mkref` ([#352](https://github.com/nf-core/scrnaseq/pull/352))
 
 ## v2.7.0 - 2024-06-03