diff --git a/modules.json b/modules.json
index 823185bc..5b4e4a3f 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "cellranger/count": {
                         "branch": "master",
-                        "git_sha": "1288cb1bff6f478affa34bf866e8ff13110607de",
+                        "git_sha": "5df79e0383386a9e43462a6e81bf978ce0a6db09",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
@@ -27,7 +27,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules"]
                     },
                     "gffread": {
@@ -57,7 +57,7 @@
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
                         "installed_by": ["modules"]
                     },
                     "universc": {
diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py
index 2172927b..1527ba76 100644
--- a/modules/nf-core/cellranger/count/templates/cellranger_count.py
+++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py
@@ -1,4 +1,9 @@
 #!/usr/bin/env python3
+"""
+Automatically rename staged files for input into cellranger count.
+
+Copyright (c) Gregor Sturm 2023 - MIT License
+"""
 from subprocess import run
 from pathlib import Path
 from textwrap import dedent
@@ -29,11 +34,11 @@ def chunk_iter(seq, size):
 # Match R1 in the filename, but only if it is followed by a non-digit or non-character
 # match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but
 # do not match "SRR12345", "file_INFIXR12", etc
-filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])"
+filename_pattern =  r'([^a-zA-Z0-9])R1([^a-zA-Z0-9])'
 
 for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2)):
     # double escapes are required because nextflow processes this python 'template'
-    if re.sub(filename_pattern, r"\\1R2\\2", r1.name) != r2.name:
+    if re.sub(filename_pattern, r'\\1R2\\2', r1.name) != r2.name:
         raise AssertionError(
             dedent(
                 f"""\
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
new file mode 100644
index 00000000..3961de60
--- /dev/null
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process FASTQC"
+    script "modules/nf-core/fastqc/main.nf"
+    process "FASTQC"
+    tag "fastqc"
+
+    test("Single-Read") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html"
+            assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>")
+            assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip"
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
index 2407d006..43424042 100644
--- a/modules/nf-core/star/genomegenerate/main.nf
+++ b/modules/nf-core/star/genomegenerate/main.nf
@@ -8,12 +8,12 @@ process STAR_GENOMEGENERATE {
         'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
 
     input:
-    path fasta
-    path gtf
+    tuple val(meta), path(fasta)
+    tuple val(meta2), path(gtf)
 
     output:
-    path "star"        , emit: index
-    path "versions.yml", emit: versions
+    tuple val(meta), path("star")  , emit: index
+    path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml
index 8181157a..eba2d9cf 100644
--- a/modules/nf-core/star/genomegenerate/meta.yml
+++ b/modules/nf-core/star/genomegenerate/meta.yml
@@ -15,14 +15,29 @@ tools:
       doi: 10.1093/bioinformatics/bts635
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Fasta file of the reference genome
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - gtf:
       type: file
       description: GTF file of the reference genome
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - index:
       type: directory
       description: Folder containing the star index files