6201 feature add stub in picardcreatesequencedictionary (nf-core#6205)

* migrate-pytest * updated snapshots * Update modules/nf-core/picard/createsequencedictionary/tests/main.nf.test Co-authored-by: Maxime U Garcia <[email protected]> * recreate snaps * Update modules/nf-core/picard/createsequencedictionary/main.nf --------- Co-authored-by: Maxime U Garcia <[email protected]>
genomic-medicine-sweden · Aug 19, 2024 · 759232f · 759232f
1 parent 29d01cb
commit 759232f
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Showing 7 changed files with 121 additions and 32 deletions.
diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf
@@ -39,4 +39,16 @@ process PICARD_CREATESEQUENCEDICTIONARY {
         picard: \$(picard CreateSequenceDictionary --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.dict
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CreateSequenceDictionary --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test
@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process PICARD_CREATESEQUENCEDICTIONARY"
+    script "../main.nf"
+    process "PICARD_CREATESEQUENCEDICTIONARY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/createsequencedictionary"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.reference_dict[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
+
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999"
+                ],
+                "reference_dict": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-19T07:02:59.686224426"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            "test.dict",
+            [
+                "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-16T14:31:34.330709472"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1121,9 +1121,6 @@ picard/collectrnaseqmetrics:
 picard/collectwgsmetrics:
   - modules/nf-core/picard/collectwgsmetrics/**
   - tests/modules/nf-core/picard/collectwgsmetrics/**
-picard/createsequencedictionary:
-  - modules/nf-core/picard/createsequencedictionary/**
-  - tests/modules/nf-core/picard/createsequencedictionary/**
 picard/fastqtosam:
   - modules/nf-core/picard/fastqtosam/**
   - tests/modules/nf-core/picard/fastqtosam/**

diff --git a/tests/modules/nf-core/picard/createsequencedictionary/main.nf b/tests/modules/nf-core/picard/createsequencedictionary/main.nf
diff --git a/tests/modules/nf-core/picard/createsequencedictionary/nextflow.config b/tests/modules/nf-core/picard/createsequencedictionary/nextflow.config
diff --git a/tests/modules/nf-core/picard/createsequencedictionary/test.yml b/tests/modules/nf-core/picard/createsequencedictionary/test.yml