Add nf-tests for markdup module

guigolab · Apr 30, 2024 · 1c47bc9 · 1c47bc9
1 parent 6bb6f20
commit 1c47bc9
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Showing 3 changed files with 87 additions and 4 deletions.
diff --git a/modules/markdup/sambamba/main.nf b/modules/markdup/sambamba/main.nf
@@ -1,5 +1,5 @@
-params.sambambaVersion = '0.7.1'
-params.container = "grapenf/sambamba:${params.sambambaVersion}"
+params.sambambaVersion = '0.7.1--h984e79f_3'
+params.container = "quay.io/biocontainers/sambamba:${params.sambambaVersion}"
 
 process markdup {
 
@@ -17,7 +17,7 @@ process markdup {
     script:
     memory = (task.memory ?: 2.GB).toMega()
     prefix = "${bam.baseName}.markdup"
-    
+
     def cmd = []
     cmd << """\
         sambamba markdup -t ${task.cpus} \\
@@ -31,4 +31,4 @@ process markdup {
         sambamba index ${prefix}.bam""".stripIndent()
 
     cmd.join('\n')
-}
+}
diff --git a/tests/modules/markdup/sambamba/main.nf.test b/tests/modules/markdup/sambamba/main.nf.test
@@ -0,0 +1,30 @@
+nextflow_process {
+
+    name "Test Process markdup"
+    script "modules/markdup/sambamba/main.nf"
+    process "markdup"
+
+    test("Should mark duplicates using sambamba") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = Channel.from([
+                    [ "sample3", "test3", file("${baseDir}/data/sample3_m4_n10_toGenome.bam"), "bam", "GenomeAlignments", true]
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
diff --git a/tests/modules/markdup/sambamba/main.nf.test.snap b/tests/modules/markdup/sambamba/main.nf.test.snap
@@ -0,0 +1,53 @@
+{
+    "Should mark duplicates using sambamba": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3_m4_n10_toGenome.markdup.bam:md5,c720dedc6b6d94a7a507543fd44b1e3a",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ],
+                "1": [
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3_m4_n10_toGenome.markdup.bam.bai:md5,9696c48348b5e0d26d4c45a211fc9bdd",
+                        "bai",
+                        "GenomeAlignmentsIndex",
+                        true
+                    ]
+                ],
+                "dedupedAlignments": [
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3_m4_n10_toGenome.markdup.bam:md5,c720dedc6b6d94a7a507543fd44b1e3a",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ],
+                "dedupedAlignmentsIndices": [
+                    [
+                        "sample3",
+                        "test3",
+                        "sample3_m4_n10_toGenome.markdup.bam.bai:md5,9696c48348b5e0d26d4c45a211fc9bdd",
+                        "bai",
+                        "GenomeAlignmentsIndex",
+                        true
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-30T19:38:12.840625"
+    }
+}