Add mirtop collapse nftest

CHANGELOG.md

@@ -12,9 +12,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#369]](https://github.com/nf-core/smrnaseq/issues/369) - Fix [Linting](https://github.com/nf-core/smrnaseq/pull/377) - Fixed linting warnings and updated modules & subworkflows.
 - [[#374]](https://github.com/nf-core/smrnaseq/pull/374) - Fix [default tests](https://github.com/nf-core/smrnaseq/issues/375) so that they do not require additional profiles in CI. Change GitHub CI fail-fast strategy to false.
 - [[#371]](https://github.com/nf-core/smrnaseq/issues/371) - Fix [Plain test profile](https://github.com/nf-core/smrnaseq/pull/372) - Updated default protocol value to "custom".
-- [[#187]](https://github.com/nf-core/smrnaseq/issues/187) - Fix checking number of samples which causes error in plotMDS.
+- [[#380]](https://github.com/nf-core/smrnaseq/pull/380) - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts: [edgeR_mirBase.R](https://github.com/nf-core/smrnaseq/issues/187).
 - [[#378]](https://github.com/nf-core/smrnaseq/pull/378) - Fix [`--mirtrace_species` bug](<(https://github.com/nf-core/smrnaseq/issues/348)>). Make `MIRTRACE` process conditional. Add mirgenedb test.
 - [[#375]](https://github.com/nf-core/smrnaseq/pull/375) - Test merging of [technical repeats](https://github.com/nf-core/smrnaseq/issues/212).
+- [[#382]](https://github.com/nf-core/smrnaseq/pull/382) - Add nf-tests for local modules using custom R scripts: [collapse_mirtop.R](https://github.com/nf-core/smrnaseq/issues/174).
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

modules/local/datatable_merge/tests/datatable_merge.nf.test

@@ -0,0 +1,71 @@
+nextflow_process {
+
+    name "Test Process TABLE_MERGE"
+    script "../datatable_merge.nf"
+    process "TABLE_MERGE"
+    tag "modules"
+    tag "modules_local"
+    tag "table_merge"
+
+    test("Contains hsa-miR-365b-3p, hsa-miR-7-5p, hsa-miR-103a-3p") {
+
+        when {
+            params {
+                outdir = "${outputDir}"
+            }
+            process {
+                """
+                input[0] = [file("https://github.com/nf-core/test-datasets/raw/smrnaseq/nf-test_data/datatable_merge/small_mirtop_dataset.txt", checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            with(process.out.mirna_tsv) {
+                with(get(0)) {
+                    assert get(0).endsWith(".tsv")
+
+                    // Check for specific miRNAs
+                    def lines = path(get(0)).readLines()
+                    assert lines.any { it.contains("hsa-miR-365b-3p") }
+                    assert lines.any { it.contains("hsa-miR-7-5p") }
+                    assert lines.any { it.contains("hsa-miR-103a-3p") }
+                }
+            }
+        }
+    }
+
+    test("Does not contain hsa-miR-107, hsa-miR-365a-3p") {
+
+        when {
+            params {
+                outdir = "${outputDir}"
+            }
+            process {
+                """
+                input[0] = [file("https://github.com/nf-core/test-datasets/raw/smrnaseq/nf-test_data/datatable_merge/small_mirtop_dataset.txt", checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            with(process.out.mirna_tsv) {
+                with(get(0)) {
+                    assert get(0).endsWith(".tsv")
+
+                    // Check for the absence of specific miRNAs
+                    def lines = path(get(0)).readLines()
+                    assert !lines.any { it.contains("hsa-miR-107") }
+                    assert !lines.any { it.contains("hsa-miR-365a-3p") }
+                }
+            }
+        }
+    }
+
+}

modules/local/datatable_merge/tests/datatable_merge.nf.test.snap

@@ -0,0 +1,48 @@
+{
+    "Contains hsa-miR-365b-3p, hsa-miR-7-5p, hsa-miR-103a-3p": {
+        "content": [
+            {
+                "0": [
+                    "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
+                ],
+                "1": [
+                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                ],
+                "mirna_tsv": [
+                    "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
+                ],
+                "versions": [
+                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T14:27:11.151441241"
+    },
+    "Does not contain hsa-miR-107, hsa-miR-365a-3p": {
+        "content": [
+            {
+                "0": [
+                    "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
+                ],
+                "1": [
+                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                ],
+                "mirna_tsv": [
+                    "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
+                ],
+                "versions": [
+                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T14:27:39.584509005"
+    }
+}

subworkflows/local/mirna_quant.nf

@@ -20,7 +20,7 @@ include {   BAM_SORT_STATS_SAMTOOLS as BAM_STATS_MATURE
 
 include { SEQCLUSTER_SEQUENCES } from '../../modules/local/seqcluster_collapse.nf'
 include { MIRTOP_QUANT         } from '../../modules/local/mirtop_quant.nf'
-include { TABLE_MERGE          } from '../../modules/local/datatable_merge.nf'
+include { TABLE_MERGE          } from '../../modules/local/datatable_merge/datatable_merge.nf'
 include { EDGER_QC             } from '../../modules/local/edger_qc/edger_qc.nf'
 
 workflow MIRNA_QUANT {