diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 903f1b03..55ae6171 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,6 +30,7 @@ jobs:
           - "test"
           - "test_no_genome"
           - "test_umi"
+          - "test_index"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4
diff --git a/conf/test_index.config b/conf/test_index.config
new file mode 100644
index 00000000..64ae5766
--- /dev/null
+++ b/conf/test_index.config
@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/smrnaseq -profile test_index,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test index profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function with bowtie index'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+
+    input            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv'
+    fasta            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'
+    bowtie_index     = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/'
+
+    mirtrace_species         = 'hsa'
+    protocol                 = 'illumina'
+    skip_mirdeep             = true
+    save_merged              = false
+    save_aligned_mirna_quant = false
+
+    cleanup                  = true //Otherwise tests dont run through properly.
+}