test: Implement nf-tests

Author: edmundmiller

.gitignore

@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+
+.nf-test*

docs/output.md

@@ -321,7 +321,6 @@ Once installed, open IGV, go to `File > Open Session` and select the `igv_sessio
 - `genome/`
   - A number of genome-specific files are generated by the pipeline in order to aid in the filtering of the data, and because they are required by standard tools such as BEDTools. These can be found in this directory along with the genome fasta file which is required by IGV. If using a genome from AWS iGenomes and if it exists a `README.txt` file containing information about the annotation version will also be saved in this directory.
 - `genome/index/`
-
   - `bwa/`: Directory containing BWA indices.
   - `bowtie2/`: Directory containing BOWTIE2 indices.
   - `chromap/`: Directory containing Chromap indices.

tests/bowtie2.nf.test

@@ -0,0 +1,48 @@
+nextflow_pipeline {
+
+    name "Test pipeline with bowtie2 aligner"
+    script "../main.nf"
+    tag "bowtie2"
+
+    test("bowtie2") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bowtie2"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size(),
+                    path("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml").readLines().first().contains("Workflow"),
+                    file("$outputDir/multiqc/multiqc_report.html").name
+                ).match() }
+            )
+        }
+    }
+
+    test("bowtie2 with stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bowtie2"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size()
+                ).match() }
+            )
+        }
+    }
+}

tests/bowtie2.nf.test.snap

@@ -0,0 +1,24 @@
+{
+    "bowtie2": {
+        "content": [
+            215,
+            false,
+            "multiqc_report.html"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-03T12:24:15.101851"
+    },
+    "bowtie2 with stub": {
+        "content": [
+            20
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-03T12:25:08.264636"
+    }
+}

tests/chromap.nf.test

@@ -0,0 +1,48 @@
+nextflow_pipeline {
+
+    name "Test pipeline with chromap aligner"
+    script "../main.nf"
+    tag "chromap"
+
+    test("chromap") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "chromap"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size(),
+                    path("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml").readLines().first().contains("Workflow"),
+                    file("$outputDir/multiqc/multiqc_report.html").name
+                ).match() }
+            )
+        }
+    }
+
+    test("chromap with stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "chromap"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size()
+                ).match() }
+            )
+        }
+    }
+}

tests/chromap.nf.test.snap

@@ -0,0 +1,24 @@
+{
+    "chromap": {
+        "content": [
+            215,
+            false,
+            "multiqc_report.html"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-03T12:24:13.69564"
+    },
+    "chromap with stub": {
+        "content": [
+            20
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-03T12:25:08.441176"
+    }
+}

tests/nextflow.config

@@ -4,8 +4,15 @@
 ========================================================================================
 */
 
-// TODO nf-core: Specify any additional parameters here
-// Or any resources requirements
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/chipseq'

tests/skip_consensus_peaks.nf.test

@@ -0,0 +1,48 @@
+nextflow_pipeline {
+
+    name "Test pipeline with --skip_consensus_peaks"
+    script "../main.nf"
+    tag "skip_consensus_peaks"
+
+    test("skip_consensus_peaks") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_consensus_peaks = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size(),
+                    path("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml").readLines().first().contains("Workflow"),
+                    file("$outputDir/multiqc/multiqc_report.html").name
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_consensus_peaks with stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_consensus_peaks = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size()
+                ).match() }
+            )
+        }
+    }
+}

tests/skip_consensus_peaks.nf.test.snap

@@ -0,0 +1,24 @@
+{
+    "skip_consensus_peaks with stub": {
+        "content": [
+            20
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-03T11:55:37.125143"
+    },
+    "skip_consensus_peaks": {
+        "content": [
+            210,
+            false,
+            "multiqc_report.html"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-03T11:55:08.155806"
+    }
+}

tests/skip_trimming.nf.test

@@ -0,0 +1,48 @@
+nextflow_pipeline {
+
+    name "Test pipeline with --skip_trimming"
+    script "../main.nf"
+    tag "skip_trimming"
+
+    test("skip_trimming") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_trimming = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size(),
+                    path("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml").readLines().first().contains("Workflow"),
+                    file("$outputDir/multiqc/multiqc_report.html").name
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_trimming with stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_trimming = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.succeeded().size()
+                ).match() }
+            )
+        }
+    }
+}