Added nf-test for gappa/examinegraft (#6519)

nf-core · Sep 2, 2024 · 406b477 · 406b477
1 parent 705b395
commit 406b477
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Showing 8 changed files with 141 additions and 36 deletions.
diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf
@@ -34,4 +34,15 @@ process GAPPA_EXAMINEGRAFT {
         gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.newick
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/gappa/examinegraft/meta.yml b/modules/nf-core/gappa/examinegraft/meta.yml
@@ -1,15 +1,17 @@
 name: "gappa_examinegraft"
-description: grafts query sequences from phylogenetic placement on the reference tree
+description: Grafts query sequences from phylogenetic placement on the reference tree
 keywords:
   - sort
+  - graft
+  - phylogeny
 tools:
   - "gappa":
       description: "Genesis Applications for Phylogenetic Placement Analysis"
       homepage: "https://github.com/lczech/gappa"
       documentation: "https://github.com/lczech/gappa/wiki"
       tool_dev_url: "https://github.com/lczech/gappa"
       doi: "10.1093/bioinformatics/btaa070"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/gappa/examinegraft/tests/main.nf.test b/modules/nf-core/gappa/examinegraft/tests/main.nf.test
@@ -0,0 +1,58 @@
+
+nextflow_process {
+
+    name "Test Process GAPPA_EXAMINEGRAFT"
+    script "../main.nf"
+    process "GAPPA_EXAMINEGRAFT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gappa"
+    tag "gappa/examinegraft"
+
+    test("test-gappa-examinegraft") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-gappa-examinegraft-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gappa/examinegraft/tests/main.nf.test.snap b/modules/nf-core/gappa/examinegraft/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "test-gappa-examinegraft-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.newick:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ea0faa432b03d6ccd726d3ba249ea5b5"
+                ],
+                "newick": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.newick:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ea0faa432b03d6ccd726d3ba249ea5b5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T12:19:44.870566"
+    },
+    "test-gappa-examinegraft": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.epa_result.newick:md5,97e54b6a9576a78b774fd63a050e5474"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ea0faa432b03d6ccd726d3ba249ea5b5"
+                ],
+                "newick": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.epa_result.newick:md5,97e54b6a9576a78b774fd63a050e5474"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ea0faa432b03d6ccd726d3ba249ea5b5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T12:19:40.543312"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -242,9 +242,6 @@ galah:
 gangstr:
   - modules/nf-core/gangstr/**
   - tests/modules/nf-core/gangstr/**
-gappa/examinegraft:
-  - modules/nf-core/gappa/examinegraft/**
-  - tests/modules/nf-core/gappa/examinegraft/**
 gatk/indelrealigner:
   - modules/nf-core/gatk/indelrealigner/**
   - tests/modules/nf-core/gatk/indelrealigner/**

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