adding nf-test file

.github/workflows/ci-tests.yml

@@ -36,4 +36,4 @@ jobs:
           sudo mv nf-test /usr/local/bin/
 
       - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
-        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }}
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} --changed-since HEAD^

tests/modules/runReadsToContig/runReadsToContig.nf.test

@@ -0,0 +1,101 @@
+nextflow_workflow {
+
+    name "Test Workflow READSTOCONTIGS"
+    script "modules/runReadsToContig/runReadsToContig.nf"
+    workflow "READSTOCONTIGS"
+
+    test("BWA mem") {
+
+        when {
+            params {
+                shared {
+                    outDir = "./testing_output"
+                    projName = "testR2C"
+                }
+                r2c {
+                    r2c_aligner = "bwa"
+                    extractUnmapped = true
+                }
+            }
+            workflow {
+                """
+                input[0] = params.r2c.plus(params.shared)
+                input[1] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
+                input[2] = file("${projectDir}/nf_assets/NO_FILE2")
+                input[3] = file("${projectDir}/test_data/contigs.fa")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert workflow.success}
+            ) 
+        }
+
+    }
+
+    test("Bowtie2") {
+
+        when {
+            params {
+                shared {
+                    outDir = "./testing_output"
+                    projName = "testR2C"
+                }
+                r2c {
+                    r2c_aligner = "bowtie2"
+                    extractUnmapped = true
+                }
+            }
+            workflow {
+                """
+                input[0] = params.r2c.plus(params.shared)
+                input[1] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
+                input[2] = file("${projectDir}/nf_assets/NO_FILE2")
+                input[3] = file("${projectDir}/test_data/contigs.fa")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert workflow.success}
+            ) 
+        }
+
+    }
+
+    test("minimap2") {
+
+        when {
+            params {
+                shared {
+                    outDir = "./testing_output"
+                    projName = "testR2C"
+                }
+                r2c {
+                    r2c_aligner = "minimap2"
+                    extractUnmapped = true
+                }
+            }
+            workflow {
+                """
+                input[0] = params.r2c.plus(params.shared)
+                input[1] = [file("${projectDir}/test_data/Ecoli_10x.1.fastq"),file("${projectDir}/test_data/Ecoli_10x.2.fastq")]
+                input[2] = file("${projectDir}/nf_assets/NO_FILE2")
+                input[3] = file("${projectDir}/test_data/contigs.fa")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert workflow.success}
+            ) 
+        }
+
+    }
+
+
+}

tests/modules/runReadsToContig/runReadsToContig.nf.test.snap

@@ -0,0 +1,14 @@
+{
+    "BWA mem": {
+        "content": [
+            "Final_contigs.fasta:md5,cfb6bc7595556231e115e5c9ad57f20d",
+            "readsToContigs_coverage.table.json:md5,ea221b314df455a84177b669edb3e5b7",
+            "readsToContigs.alnstats.txt:md5,259f501e745b79cb92b69e335d01cac7"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-17T13:52:25.552513444"
+    }
+}