Add prefix to output file for barrnap (#5919)

* Add prefix to output file * Update barrnap to nf-test * Update tags.yml * Add missing bracket and run test * Correct format of license * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Review suggestions * Prettier * Update meta.yml * Update tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
nf-core · Jul 11, 2024 · c4c7ecb · c4c7ecb
1 parent 0dee12b
commit c4c7ecb
Show file tree

Hide file tree

Showing 9 changed files with 138 additions and 35 deletions.
diff --git a/modules/nf-core/barrnap/main.nf b/modules/nf-core/barrnap/main.nf
@@ -32,7 +32,7 @@ process BARRNAP {
         --threads $task.cpus \\
         --kingdom $db \\
         $input \\
-        > rrna_${db}.gff
+        > ${prefix}_${db}.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,9 +44,9 @@ process BARRNAP {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    db = dbname ? "${dbname}" : 'bac'
     """
-    touch ${prefix}.gff
+    touch ${prefix}_${db}.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/barrnap/meta.yml b/modules/nf-core/barrnap/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/tseemann/barrnap"
       documentation: "https://github.com/tseemann/barrnap"
       tool_dev_url: "https://github.com/tseemann/barrnap"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -23,6 +23,9 @@ input:
       type: file
       description: fastq or fasta file nucleotides (it can be amino acids as well)
       pattern: "*.{fna,fasta,faa,fastq}"
+  - dbname:
+      type: string
+      description: database to use(bacteria, archaea, eukaryota, metazoan mitochondria)
 output:
   - meta:
       type: map

diff --git a/modules/nf-core/barrnap/tests/main.nf.test b/modules/nf-core/barrnap/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process BARRNAP"
+    script "../main.nf"
+    process "BARRNAP"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "barrnap"
+
+    test("barrnap") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                                "bac"
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("barrnap - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                                "bac"
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
+
+
diff --git a/modules/nf-core/barrnap/tests/main.nf.test.snap b/modules/nf-core/barrnap/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "barrnap - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-10T11:25:35.085998"
+    },
+    "barrnap": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-10T11:25:28.621027"
+    }
+}
diff --git a/modules/nf-core/barrnap/tests/tags.yml b/modules/nf-core/barrnap/tests/tags.yml
@@ -0,0 +1,2 @@
+barrnap:
+  - "modules/nf-core/barrnap/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -70,9 +70,6 @@ bamutil/trimbam:
 bandage/image:
   - modules/nf-core/bandage/image/**
   - tests/modules/nf-core/bandage/image/**
-barrnap:
-  - modules/nf-core/barrnap/**
-  - tests/modules/nf-core/barrnap/**
 basicpy:
   - modules/nf-core/basicpy/**
   - tests/modules/nf-core/basicpy/**

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