From 00b6314523f8a16934978ae67c25c341b3ddba05 Mon Sep 17 00:00:00 2001
From: Fattigman <jacob.karlstrom@gmail.com>
Date: Tue, 17 Oct 2023 12:29:31 +0200
Subject: [PATCH 1/2] Added nextflow conf for cellranger argument

---
 modules/cellranger/count-atac/main.nf    | 2 +-
 modules/cellranger/count-citeseq/main.nf | 1 +
 modules/cellranger/count-rna/main.nf     | 2 +-
 nextflow.config                          | 1 +
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/cellranger/count-atac/main.nf b/modules/cellranger/count-atac/main.nf
index 1434ee2..5cb492e 100644
--- a/modules/cellranger/count-atac/main.nf
+++ b/modules/cellranger/count-atac/main.nf
@@ -43,7 +43,7 @@ process COUNT_ATAC {
 	     --sample=$sample_id \\
 	     --reference=$genome \\
 		--localcores=19 --localmem=120 \\
-		 $forcecells $intron_argument
+		 $forcecells $intron_argument $params.cellranger_arguments
 
 	"""
 	stub:
diff --git a/modules/cellranger/count-citeseq/main.nf b/modules/cellranger/count-citeseq/main.nf
index cad5604..4d77a5f 100644
--- a/modules/cellranger/count-citeseq/main.nf
+++ b/modules/cellranger/count-citeseq/main.nf
@@ -36,6 +36,7 @@ process COUNT {
          --feature-ref=$feature_reference \\
          --libraries=$library \\
 		 --localcores=19 --localmem=120 \\
+		 $params.cellranger_arguments
 
 	"""
 	stub:
diff --git a/modules/cellranger/count-rna/main.nf b/modules/cellranger/count-rna/main.nf
index 31816c4..0e15aae 100644
--- a/modules/cellranger/count-rna/main.nf
+++ b/modules/cellranger/count-rna/main.nf
@@ -41,7 +41,7 @@ process COUNT {
 	     --sample $sample_id \\
 	     --transcriptome $genome \\
 		--localcores=19 --localmem 120 \\
-		 $forcecells $intron_argument
+		 $forcecells $intron_argument $params.cellranger_arguments
 
 	"""
 	stub:
diff --git a/nextflow.config b/nextflow.config
index edd7700..582df58 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -43,6 +43,7 @@ params {
 	// runOptions
 	intron_mode="true"
 	ctg_mode="true"
+	cellranger_arguments=""
 	
 	deliver_to = "henning.onsbring@med.lu.se"
 

From ff7b35aabd77f5e5b48ebd235c35dedbb0c2665d Mon Sep 17 00:00:00 2001
From: Fattigman <jacob.karlstrom@gmail.com>
Date: Tue, 17 Oct 2023 12:31:23 +0200
Subject: [PATCH 2/2] added cellranger arguments for multi

---
 modules/cellranger/count-arc/main.nf | 1 +
 modules/cellranger/multi/main.nf     | 1 +
 2 files changed, 2 insertions(+)

diff --git a/modules/cellranger/count-arc/main.nf b/modules/cellranger/count-arc/main.nf
index 898f5d3..e0ca44c 100644
--- a/modules/cellranger/count-arc/main.nf
+++ b/modules/cellranger/count-arc/main.nf
@@ -31,6 +31,7 @@ process COUNT_ARC {
 	     --reference=$genome \\
          --libraries=$library \\
 		 --localcores=19 --localmem=120 \\
+		 $params.cellranger_arguments
 
 	"""
 	stub:
diff --git a/modules/cellranger/multi/main.nf b/modules/cellranger/multi/main.nf
index e3a4ff5..9e59d9f 100644
--- a/modules/cellranger/multi/main.nf
+++ b/modules/cellranger/multi/main.nf
@@ -18,6 +18,7 @@ process MULTI {
 	     --id=$sample_id \\
          --csv=$config \\
 		--localcores=16 --localmem=120 \\
+		$params.cellranger_arguments
 	"""
 	stub:
 	"""