Migration test cutadapt (nf-core#4072)

* migrate cutadapt test to modules * add cutadapt pytest * fix typo * fix minor typo * remove cutadapt pytest * remove modules.yml * add tags.yml * fixed paired reads test * updated snap * using filtering for output gz * Update single-read test name Co-authored-by: Sateesh_Peri <[email protected]> * Update paired-reads test name Co-authored-by: Sateesh_Peri <[email protected]> --------- Co-authored-by: Sateesh_Peri <[email protected]>
maxulysse · Nov 24, 2023 · 07881e4 · 07881e4
1 parent 485558b
commit 07881e4
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Showing 5 changed files with 100 additions and 4 deletions.
diff --git a/modules/nf-core/cutadapt/tests/main.nf.test b/modules/nf-core/cutadapt/tests/main.nf.test
@@ -0,0 +1,69 @@
+nextflow_process {
+
+    name "Test Process CUTADAPT"
+    script "../main.nf"
+    process "CUTADAPT"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cutadapt"
+
+    test("sarscov2 Illumina single end [fastq]") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.reads != null },
+                { assert process.out.reads.get(0).get(1) ==~ ".*.trim.fastq.gz" },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert snapshot(path(process.out.reads.get(0).get(1)).linesGzip[0]).match() }
+            )
+        }
+    }
+
+    test("sarscov2 Illumina paired-end [fastq]") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:false ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.reads != null },
+                { assert process.out.reads.get(0).get(1).get(0) ==~ ".*.1.trim.fastq.gz" },
+                { assert process.out.reads.get(0).get(1).get(1) ==~ ".*.2.trim.fastq.gz" },
+                { assert snapshot(path(process.out.reads.get(0).get(1).get(1)).linesGzip[0]).match() },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/cutadapt/tests/main.nf.test.snap b/modules/nf-core/cutadapt/tests/main.nf.test.snap
diff --git a/modules/nf-core/cutadapt/tests/nextflow.config b/modules/nf-core/cutadapt/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: CUTADAPT {
+        ext.args = '-q 25'
+    }
+
+}
diff --git a/modules/nf-core/cutadapt/tests/tags.yml b/modules/nf-core/cutadapt/tests/tags.yml
@@ -0,0 +1,2 @@
+cutadapt:
+  - modules/nf-core/cutadapt/**
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -811,10 +811,6 @@ custom/tabulartogseagct:
   - modules/nf-core/custom/tabulartogseagct/**
   - tests/modules/nf-core/custom/tabulartogseagct/**
 
-cutadapt:
-  - modules/nf-core/cutadapt/**
-  - tests/modules/nf-core/cutadapt/**
-
 cutesv:
   - modules/nf-core/cutesv/**
   - tests/modules/nf-core/cutesv/**