diff --git a/workflows/tests/inputs/uniqmap/main.nf.test b/workflows/tests/inputs/uniqmap/main.nf.test
new file mode 100644
index 00000000..65a67030
--- /dev/null
+++ b/workflows/tests/inputs/uniqmap/main.nf.test
@@ -0,0 +1,52 @@
+nextflow_pipeline {
+
+    name "HOMER Uniqmap"
+    script "../../../../main.nf"
+    tag "input"
+    tag "homer"
+
+    test("Should run with an zipped uniqmap") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                use_homer_uniqmap = true
+                homer_uniqmap = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/uniqmap.GRCh38_chr21.50nt.zip'
+                skip_grohmm = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
+                    // Files should have -uniqmap <directory> in the header
+                { assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[18].contains("uniqMapDirectory = uniqmap.GRCh38_chr21.50nt") },
+                { assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[20].contains("-uniqmap") },
+                { assert path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[18].contains("uniqMapDirectory = uniqmap.GRCh38_chr21.50nt") },
+                { assert path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[20].contains("-uniqmap") },
+                    // TODO Test for uniqmap unzip process
+                // { assert workflow.trace.tasks().find { it.process == "UNZIP" } },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                    path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[18],
+                    path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[20],
+                    path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[18],
+                    path("$outputDir/transcript_identification/homer/jurkat.bed").readLines()[20],
+                    path("$outputDir/transcript_identification/homer/cd4.bed"),
+                    path("$outputDir/transcript_identification/homer/jurkat.bed"),
+                    path("$outputDir/transcript_identification/homer/cd4-uniqmap.GRCh38_chr21.peaks.txt"),
+                    path("$outputDir/transcript_identification/homer/jurkat-uniqmap.GRCh38_chr21.peaks.txt"),
+                    path("$outputDir/transcript_identification/intersect/").list(),
+                    path("$outputDir/transcript_identification/filtered/").list(),
+                    // FIXME Not determinstic because of the order of files
+                    // Add to the other tests when fixed
+                    // path("$outputDir/quantification/").list(),
+                    path("$outputDir/multiqc/multiqc_report.html").exists(),
+                ).match("output_files")
+                }
+            )
+        }
+    }
+    // TODO Check for running with unzipped uniqmap
+}
diff --git a/workflows/tests/inputs/uniqmap/main.nf.test.snap b/workflows/tests/inputs/uniqmap/main.nf.test.snap
new file mode 100644
index 00000000..239af9b2
--- /dev/null
+++ b/workflows/tests/inputs/uniqmap/main.nf.test.snap
@@ -0,0 +1,125 @@
+{
+    "output_files": {
+        "content": [
+            93,
+            "# uniqMapDirectory = uniqmap.GRCh38_chr21.50nt",
+            "# cmd = findPeaks cd4_tagdir -style groseq -o cd4-uniqmap.GRCh38_chr21.peaks.txt -uniqmap uniqmap.GRCh38_chr21.50nt",
+            "# uniqMapDirectory = uniqmap.GRCh38_chr21.50nt",
+            "# cmd = findPeaks jurkat_tagdir -style groseq -o jurkat-uniqmap.GRCh38_chr21.peaks.txt -uniqmap uniqmap.GRCh38_chr21.50nt",
+            "cd4.bed:md5,bbe77431f7c1ac833d1f939012435962",
+            "jurkat.bed:md5,98dd0b5dde7b11c0604b35c391754c9d",
+            "cd4-uniqmap.GRCh38_chr21.peaks.txt:md5,bbe77431f7c1ac833d1f939012435962",
+            "jurkat-uniqmap.GRCh38_chr21.peaks.txt:md5,98dd0b5dde7b11c0604b35c391754c9d",
+            [
+                "cd4_intersect.bed:md5,a5d31a685d89293ae64daff9a9054568",
+                "jurkat_intersect.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "cd4_filtered.bed:md5,fe48a92889bc118c41e436989f85c65e",
+                "jurkat_filtered.bed:md5,f1dde43c4ad9dec972ff9fa38cc6f2fe"
+            ],
+            true
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T14:08:33.633789"
+    },
+    "software_versions": {
+        "content": [
+            {
+                "BBMAP_PILEUP": {
+                    "bbmap": 39.01,
+                    "samtools": "1.16.1",
+                    "pigz": 2.6
+                },
+                "BEDTOOLS_GENOMECOV_MINUS": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_GENOMECOV_PLUS": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_INTERSECT": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_INTERSECT_FILTER": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_MERGE": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_SORT": {
+                    "bedtools": "2.31.1"
+                },
+                "BWA_INDEX": {
+                    "bwa": "0.7.18-r1243-dirty"
+                },
+                "BWA_MEM": {
+                    "bwa": "0.7.18-r1243-dirty",
+                    "samtools": 1.2
+                },
+                "CAT_CAT": {
+                    "pigz": "2.3.4"
+                },
+                "CUSTOM_GETCHROMSIZES": {
+                    "getchromsizes": 1.2
+                },
+                "DEEPTOOLS_BAMCOVERAGE_MINUS": {
+                    "deeptools": "3.5.1"
+                },
+                "DEEPTOOLS_BAMCOVERAGE_PLUS": {
+                    "deeptools": "3.5.1"
+                },
+                "FASTP": {
+                    "fastp": "0.23.4"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "GTF2BED": {
+                    "perl": "5.26.2"
+                },
+                "PINTS_CALLER": {
+                    "python": "3.12.6",
+                    "pints": "1.1.13"
+                },
+                "PRESEQ_CCURVE": {
+                    "preseq": "3.1.1"
+                },
+                "PRESEQ_LCEXTRAP": {
+                    "preseq": "3.1.1"
+                },
+                "RSEQC_INFEREXPERIMENT": {
+                    "rseqc": "5.0.2"
+                },
+                "RSEQC_READDISTRIBUTION": {
+                    "rseqc": "5.0.2"
+                },
+                "RSEQC_READDUPLICATION": {
+                    "rseqc": "5.0.2"
+                },
+                "SAMTOOLS_MERGE": {
+                    "samtools": 1.21
+                },
+                "SUBREAD_FEATURECOUNTS_GENE": {
+                    "subread": "2.0.1"
+                },
+                "SUBREAD_FEATURECOUNTS_PREDICTED": {
+                    "subread": "2.0.1"
+                },
+                "UNZIP": {
+                    "7za": 16.02
+                },
+                "Workflow": {
+                    "nf-core/nascent": "v2.3.0dev"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T10:49:29.60087"
+    }
+}
\ No newline at end of file