diff --git a/.gitignore b/.gitignore
index 61b9470a..bc675aba 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@ log/
 reports/
 testme.sh
 .nf-test*
+.vscode
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a9d9a7e7..51953318 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Change from pytests to nf-test ([#291](https://github.com/nf-core/scrnaseq/pull/291))
 - Update template to v2.13.1 ([#309](https://github.com/nf-core/scrnaseq/pull/309))
 - Update to kallisto|bustools v0.28.2 ([#294](https://github.com/nf-core/scrnaseq/pull/294))
+- Fix cellrangerarc matrix conversions and protocol selection ([#300](https://github.com/nf-core/scrnaseq/pull/300))
 
 ## v2.5.1
 
diff --git a/assets/protocols.json b/assets/protocols.json
index 23ff1328..d8da2f8a 100644
--- a/assets/protocols.json
+++ b/assets/protocols.json
@@ -30,6 +30,11 @@
             "protocol": "SC3Pv3"
         }
     },
+    "cellrangerarc": {
+        "auto": {
+            "protocol": "auto"
+        }
+    },
     "star": {
         "10XV1": {
             "protocol": "CB_UMI_Simple",
diff --git a/modules.json b/modules.json
index 6040254b..32171104 100644
--- a/modules.json
+++ b/modules.json
@@ -22,7 +22,7 @@
                     },
                     "cellrangerarc/count": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "18e53e27cfeca5dbbfbeee675c05438dec68245f",
                         "installed_by": ["modules"]
                     },
                     "cellrangerarc/mkgtf": {
@@ -42,7 +42,7 @@
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
diff --git a/modules/nf-core/cellrangerarc/count/main.nf b/modules/nf-core/cellrangerarc/count/main.nf
index 2bf0193a..e5ce9225 100644
--- a/modules/nf-core/cellrangerarc/count/main.nf
+++ b/modules/nf-core/cellrangerarc/count/main.nf
@@ -14,9 +14,9 @@ process CELLRANGERARC_COUNT {
     path  reference
 
     output:
-    tuple val(meta), path("${meta.id}/outs/*"), emit: outs
-    path("${meta.id}_lib.csv")                , emit: lib
-    path "versions.yml"                       , emit: versions
+    tuple val(meta), path("${meta.id}/outs/**"), emit: outs
+    path("${meta.id}_lib.csv")                 , emit: lib
+    path "versions.yml"                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test
index bdbc96ae..452aba1b 100644
--- a/modules/nf-core/gffread/tests/main.nf.test
+++ b/modules/nf-core/gffread/tests/main.nf.test
@@ -38,6 +38,8 @@ nextflow_process {
 
     test("sarscov2-gff3-gff3") {
 
+        config "./nextflow-gff3.config"
+
         when {
             params {
                 outdir = "$outputDir"
diff --git a/modules/nf-core/gffread/tests/nextflow-gff3.config b/modules/nf-core/gffread/tests/nextflow-gff3.config
new file mode 100644
index 00000000..afe0830e
--- /dev/null
+++ b/modules/nf-core/gffread/tests/nextflow-gff3.config
@@ -0,0 +1,5 @@
+process {
+    withName: GFFREAD {
+        ext.args = ''
+    }
+}