diff --git a/conf/modules.config b/conf/modules.config
index 2d1265d..113c937 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -47,7 +47,6 @@ process {
     }
 
     withName: SPACERANGER_COUNT {
-        ext.args = '--create-bam false'
         publishDir = [
             path: { "${params.outdir}/${meta.id}/spaceranger" },
             mode: params.publish_dir_mode,
diff --git a/modules.json b/modules.json
index 6d76717..4031514 100644
--- a/modules.json
+++ b/modules.json
@@ -25,7 +25,8 @@
                     "spaceranger/count": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/spaceranger/count/spaceranger-count.diff"
                     },
                     "untar": {
                         "branch": "master",
diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml
index e1ffcef..17626e1 100644
--- a/modules/nf-core/spaceranger/count/meta.yml
+++ b/modules/nf-core/spaceranger/count/meta.yml
@@ -24,58 +24,57 @@ tools:
         - "10x Genomics EULA"
       identifier: ""
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', slide:'10L13-020', area: 'B1']
-
-          `id`, `slide` and `area` are mandatory information!
-    - reads:
-        type: file
-        description: |
-          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-          respectively.
-        pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz"
-    - image:
-        type: file
-        description: Brightfield tissue H&E image in JPEG or TIFF format.
-        pattern: "*.{tif,tiff,jpg,jpeg}"
-    - cytaimage:
-        type: file
-        description: |
-          CytAssist instrument captured eosin stained Brightfield tissue image with fiducial
-          frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should
-          not be modified any way before passing it as input to either Space Ranger or Loupe Browser.
-        pattern: "*.{tif,tiff}"
-    - darkimage:
-        type: file
-        description: |
-          Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence
-          image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.
-        pattern: "*.{tif,tiff,jpg,jpeg}"
-    - colorizedimage:
-        type: file
-        description: |
-          Required for color composite fluorescence microscope image input.
-          A color composite of one or more fluorescence image channels saved as a single-page,
-          single-file color TIFF or JPEG.
-        pattern: "*.{tif,tiff,jpg,jpeg}"
-    - alignment:
-        type: file
-        description: OPTIONAL - Path to manual image alignment.
-        pattern: "*.json"
-    - slidefile:
-        type: file
-        description: OPTIONAL - Path to slide specifications.
-        pattern: "*.json"
-  - - reference:
-        type: directory
-        description: Folder containing all the reference indices needed by Space Ranger
-  - - probeset:
-        type: file
-        description: OPTIONAL - Probe set specification.
-        pattern: "*.csv"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', slide:'10L13-020', area: 'B1']
+        `id`, `slide` and `area` are mandatory information!
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+      pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz"
+  - image:
+      type: file
+      description: Brightfield tissue H&E image in JPEG or TIFF format.
+      pattern: "*.{tif,tiff,jpg,jpeg}"
+  - cytaimage:
+      type: file
+      description: |
+        CytAssist instrument captured eosin stained Brightfield tissue image with fiducial
+        frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should
+        not be modified any way before passing it as input to either Space Ranger or Loupe Browser.
+      pattern: "*.{tif,tiff}"
+  - darkimage:
+      type: file
+      description: |
+        Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence
+        image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.
+      pattern: "*.{tif,tiff,jpg,jpeg}"
+  - colorizedimage:
+      type: file
+      description: |
+        Required for color composite fluorescence microscope image input.
+        A color composite of one or more fluorescence image channels saved as a single-page,
+        single-file color TIFF or JPEG.
+      pattern: "*.{tif,tiff,jpg,jpeg}"
+  - alignment:
+      type: file
+      description: OPTIONAL - Path to manual image alignment.
+      pattern: "*.json"
+  - slidefile:
+      type: file
+      description: OPTIONAL - Path to slide specifications.
+      pattern: "*.json"
+  - reference:
+      type: directory
+      description: Folder containing all the reference indices needed by Space Ranger
+  - probeset:
+      type: file
+      description: OPTIONAL - Probe set specification.
+      pattern: "*.csv"
 output:
   - outs:
       - meta:
diff --git a/modules/nf-core/spaceranger/count/modules.json b/modules/nf-core/spaceranger/count/modules.json
new file mode 100644
index 0000000..02a6334
--- /dev/null
+++ b/modules/nf-core/spaceranger/count/modules.json
@@ -0,0 +1,5 @@
+{
+    "name": "",
+    "homePage": "",
+    "repos": {}
+}
diff --git a/modules/nf-core/spaceranger/count/spaceranger-count.diff b/modules/nf-core/spaceranger/count/spaceranger-count.diff
new file mode 100644
index 0000000..141c0e5
--- /dev/null
+++ b/modules/nf-core/spaceranger/count/spaceranger-count.diff
@@ -0,0 +1,132 @@
+Changes in module 'nf-core/spaceranger/count'
+Changes in 'spaceranger/count/meta.yml':
+--- modules/nf-core/spaceranger/count/meta.yml
++++ modules/nf-core/spaceranger/count/meta.yml
+@@ -24,58 +24,57 @@
+         - "10x Genomics EULA"
+       identifier: ""
+ input:
+-  - - meta:
+-        type: map
+-        description: |
+-          Groovy Map containing sample information
+-          e.g. [ id:'test', slide:'10L13-020', area: 'B1']
+-
+-          `id`, `slide` and `area` are mandatory information!
+-    - reads:
+-        type: file
+-        description: |
+-          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+-          respectively.
+-        pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz"
+-    - image:
+-        type: file
+-        description: Brightfield tissue H&E image in JPEG or TIFF format.
+-        pattern: "*.{tif,tiff,jpg,jpeg}"
+-    - cytaimage:
+-        type: file
+-        description: |
+-          CytAssist instrument captured eosin stained Brightfield tissue image with fiducial
+-          frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should
+-          not be modified any way before passing it as input to either Space Ranger or Loupe Browser.
+-        pattern: "*.{tif,tiff}"
+-    - darkimage:
+-        type: file
+-        description: |
+-          Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence
+-          image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.
+-        pattern: "*.{tif,tiff,jpg,jpeg}"
+-    - colorizedimage:
+-        type: file
+-        description: |
+-          Required for color composite fluorescence microscope image input.
+-          A color composite of one or more fluorescence image channels saved as a single-page,
+-          single-file color TIFF or JPEG.
+-        pattern: "*.{tif,tiff,jpg,jpeg}"
+-    - alignment:
+-        type: file
+-        description: OPTIONAL - Path to manual image alignment.
+-        pattern: "*.json"
+-    - slidefile:
+-        type: file
+-        description: OPTIONAL - Path to slide specifications.
+-        pattern: "*.json"
+-  - - reference:
+-        type: directory
+-        description: Folder containing all the reference indices needed by Space Ranger
+-  - - probeset:
+-        type: file
+-        description: OPTIONAL - Probe set specification.
+-        pattern: "*.csv"
++  - meta:
++      type: map
++      description: |
++        Groovy Map containing sample information
++        e.g. [ id:'test', slide:'10L13-020', area: 'B1']
++        `id`, `slide` and `area` are mandatory information!
++  - reads:
++      type: file
++      description: |
++        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
++        respectively.
++      pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz"
++  - image:
++      type: file
++      description: Brightfield tissue H&E image in JPEG or TIFF format.
++      pattern: "*.{tif,tiff,jpg,jpeg}"
++  - cytaimage:
++      type: file
++      description: |
++        CytAssist instrument captured eosin stained Brightfield tissue image with fiducial
++        frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should
++        not be modified any way before passing it as input to either Space Ranger or Loupe Browser.
++      pattern: "*.{tif,tiff}"
++  - darkimage:
++      type: file
++      description: |
++        Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence
++        image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.
++      pattern: "*.{tif,tiff,jpg,jpeg}"
++  - colorizedimage:
++      type: file
++      description: |
++        Required for color composite fluorescence microscope image input.
++        A color composite of one or more fluorescence image channels saved as a single-page,
++        single-file color TIFF or JPEG.
++      pattern: "*.{tif,tiff,jpg,jpeg}"
++  - alignment:
++      type: file
++      description: OPTIONAL - Path to manual image alignment.
++      pattern: "*.json"
++  - slidefile:
++      type: file
++      description: OPTIONAL - Path to slide specifications.
++      pattern: "*.json"
++  - reference:
++      type: directory
++      description: Folder containing all the reference indices needed by Space Ranger
++  - probeset:
++      type: file
++      description: OPTIONAL - Probe set specification.
++      pattern: "*.csv"
+ output:
+   - outs:
+       - meta:
+
+'modules/nf-core/spaceranger/count/modules.json' was created
+'modules/nf-core/spaceranger/count/main.nf' is unchanged
+'modules/nf-core/spaceranger/count/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/spaceranger/count/tests/tags.yml' is unchanged
+Changes in 'spaceranger/count/tests/nextflow.config':
+--- modules/nf-core/spaceranger/count/tests/nextflow.config
++++ modules/nf-core/spaceranger/count/tests/nextflow.config
+@@ -1,5 +1,5 @@
+ process {
+     withName: SPACERANGER_COUNT {
+-        ext.args = '--create-bam false'
++        ext.args = '--create-bam="false"'
+     }
+ }
+
+'modules/nf-core/spaceranger/count/tests/main.nf.test' is unchanged
+************************************************************
diff --git a/modules/nf-core/spaceranger/count/tests/nextflow.config b/modules/nf-core/spaceranger/count/tests/nextflow.config
index fe9d61a..e4b3571 100644
--- a/modules/nf-core/spaceranger/count/tests/nextflow.config
+++ b/modules/nf-core/spaceranger/count/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: SPACERANGER_COUNT {
-        ext.args = '--create-bam false'
+        ext.args = '--create-bam="false"'
     }
 }