Bump concoct/cutupfasta version, add stub, add nf-test (#5864)

* Bump concoct/cutupfasta version, add stub, add nf-test * Fix linting
nf-core · Jun 21, 2024 · 73a6d7e · 73a6d7e
1 parent f958600
commit 73a6d7e
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Showing 9 changed files with 163 additions and 37 deletions.
diff --git a/modules/nf-core/concoct/cutupfasta/main.nf b/modules/nf-core/concoct/cutupfasta/main.nf
@@ -5,8 +5,8 @@ process CONCOCT_CUTUPFASTA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4':
-        'biocontainers/concoct:1.1.0--py311h245ed52_4' }"
+        'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py312h245ed52_6':
+        'biocontainers/concoct:1.1.0--py312h245ed52_6' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -37,4 +37,18 @@ process CONCOCT_CUTUPFASTA {
         concoct: \$(echo \$(concoct --version 2>&1) | sed 's/concoct //g' )
     END_VERSIONS
     """
+
+    stub:
+    def args       = task.ext.args ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def bedfile    = bed ? "-b ${prefix}.bed" : ""
+    if ("$fasta" == "${prefix}.fasta") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    """
+    touch ${prefix}.fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        concoct: \$(echo \$(concoct --version 2>&1) | sed 's/concoct //g' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/concoct/cutupfasta/meta.yml b/modules/nf-core/concoct/cutupfasta/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: "https://concoct.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/BinPro/CONCOCT"
       doi: "10.1038/nmeth.3103"
-      licence: "['FreeBSD']"
+      licence: ["FreeBSD"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/concoct/cutupfasta/tests/main.nf.test b/modules/nf-core/concoct/cutupfasta/tests/main.nf.test
@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process CONCOCT_CUTUPFASTA"
+    script "../main.nf"
+    process "CONCOCT_CUTUPFASTA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "concoct"
+    tag "concoct/cutupfasta"
+
+    test("sarscov2 - genome - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [id: 'test', single_end: false],
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [id: 'test', single_end: false],
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/concoct/cutupfasta/tests/main.nf.test.snap b/modules/nf-core/concoct/cutupfasta/tests/main.nf.test.snap
@@ -0,0 +1,84 @@
+{
+    "sarscov2 - genome - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,b7d972e6efa0b306e02e46a685310c7f"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,9785f4f0f5f6e8d020a52a9e2c4fa3e0"
+                ],
+                "bed": [
+
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,b7d972e6efa0b306e02e46a685310c7f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9785f4f0f5f6e8d020a52a9e2c4fa3e0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T15:13:08.126117371"
+    },
+    "sarscov2 - genome - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,9785f4f0f5f6e8d020a52a9e2c4fa3e0"
+                ],
+                "bed": [
+
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9785f4f0f5f6e8d020a52a9e2c4fa3e0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T15:13:20.929503446"
+    }
+}
diff --git a/modules/nf-core/concoct/cutupfasta/tests/tags.yml b/modules/nf-core/concoct/cutupfasta/tests/tags.yml
@@ -0,0 +1,2 @@
+concoct/cutupfasta:
+  - "modules/nf-core/concoct/cutupfasta/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -287,9 +287,6 @@ concoct/concoct:
 concoct/concoctcoveragetable:
   - modules/nf-core/concoct/concoctcoveragetable/**
   - tests/modules/nf-core/concoct/concoctcoveragetable/**
-concoct/cutupfasta:
-  - modules/nf-core/concoct/cutupfasta/**
-  - tests/modules/nf-core/concoct/cutupfasta/**
 concoct/extractfastabins:
   - modules/nf-core/concoct/extractfastabins/**
   - tests/modules/nf-core/concoct/extractfastabins/**

diff --git a/tests/modules/nf-core/concoct/cutupfasta/main.nf b/tests/modules/nf-core/concoct/cutupfasta/main.nf
diff --git a/tests/modules/nf-core/concoct/cutupfasta/nextflow.config b/tests/modules/nf-core/concoct/cutupfasta/nextflow.config
diff --git a/tests/modules/nf-core/concoct/cutupfasta/test.yml b/tests/modules/nf-core/concoct/cutupfasta/test.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		concoct/cutupfasta:
		- "modules/nf-core/concoct/cutupfasta/**"