From d587915b2307cf1f91f9c915c4ad96c4e52ce68c Mon Sep 17 00:00:00 2001
From: Andre Watson <andre.watson22@gmail.com>
Date: Tue, 17 Dec 2024 14:00:59 -0700
Subject: [PATCH] adding nf-test file

---
 .github/workflows/ci-tests.yml                |   2 +-
 .../runReadsToContig/runReadsToContig.nf.test | 101 ++++++++++++++++++
 .../runReadsToContig.nf.test.snap             |  14 +++
 3 files changed, 116 insertions(+), 1 deletion(-)
 create mode 100644 tests/modules/runReadsToContig/runReadsToContig.nf.test
 create mode 100644 tests/modules/runReadsToContig/runReadsToContig.nf.test.snap

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 3a049c4..4c63f4a 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.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 }}
\ No newline at end of file
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} --changed-since HEAD^
\ No newline at end of file
diff --git a/tests/modules/runReadsToContig/runReadsToContig.nf.test b/tests/modules/runReadsToContig/runReadsToContig.nf.test
new file mode 100644
index 0000000..3933515
--- /dev/null
+++ b/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}
+            ) 
+        }
+
+    }
+
+
+}
diff --git a/tests/modules/runReadsToContig/runReadsToContig.nf.test.snap b/tests/modules/runReadsToContig/runReadsToContig.nf.test.snap
new file mode 100644
index 0000000..cc4cc37
--- /dev/null
+++ b/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"
+    }
+}
\ No newline at end of file