diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml
index d4034576..9cfcfa55 100644
--- a/.github/workflows/fastqc.yml
+++ b/.github/workflows/fastqc.yml
@@ -12,6 +12,7 @@ jobs:
 
     # Check out the repository
     - uses: actions/checkout@v1
+      submodules: true
 
     - name: Install Nextflow
       run: |
diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml
index c49bbec6..302e0b6d 100644
--- a/.github/workflows/samtools_index.yml
+++ b/.github/workflows/samtools_index.yml
@@ -12,6 +12,7 @@ jobs:
 
     # Check out the repository
     - uses: actions/checkout@v1
+      submodules: true
 
     - name: Install Nextflow
       run: |
diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml
index f6e0ac4c..cc9ce4f8 100644
--- a/.github/workflows/samtools_sort.yml
+++ b/.github/workflows/samtools_sort.yml
@@ -12,6 +12,7 @@ jobs:
 
     # Check out the repository
     - uses: actions/checkout@v1
+      submodules: true
 
     - name: Install Nextflow
       run: |
diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml
index 033ae6ec..d914313e 100644
--- a/.github/workflows/trim_galore.yml
+++ b/.github/workflows/trim_galore.yml
@@ -12,6 +12,7 @@ jobs:
 
     # Check out the repository
     - uses: actions/checkout@v1
+      submodules: true
 
     - name: Install Nextflow
       run: |
diff --git a/tools/fastqc/test/main.nf b/tools/fastqc/test/main.nf
index 6ab43b7b..f24a81da 100644
--- a/tools/fastqc/test/main.nf
+++ b/tools/fastqc/test/main.nf
@@ -5,9 +5,10 @@ include '../main.nf' params(params)
 
 // Define input channels
 readPaths = [
-  ['SRR389222_sub1', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz']],
-  ['SRR389222_sub2', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']],
-  ['SRR389222_sub3', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz']]
+  ['SRR4238351', ['../../../test-datasets/tools/fastqc/input/SRR4238351_subsamp.fastq.gz']],
+  ['SRR4238355', ['../../../test-datasets/tools/fastqc/input/SRR4238355_subsamp.fastq.gz']],
+  ['SRR4238359', ['../../../test-datasets/tools/fastqc/input/SRR4238359_subsamp.fastq.gz']],
+  ['SRR4238379', ['../../../test-datasets/tools/fastqc/input/SRR4238379_subsamp.fastq.gz']]
 ]
 Channel
   .from(readPaths)