Added nf-test for ivar/consensus (#6568)

* Added nf-test for ivar/consensus

* Verion bump

modules/nf-core/ivar/consensus/environment.yml

@@ -2,6 +2,5 @@ name: ivar_consensus
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::ivar=1.4
+  - bioconda::ivar=1.4.3

modules/nf-core/ivar/consensus/main.nf

@@ -4,8 +4,8 @@ process IVAR_CONSENSUS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' :
-        'biocontainers/ivar:1.4--h6b7c446_1' }"
+        'https://depot.galaxyproject.org/singularity/ivar:1.4.3--h43eeafb_0' :
+        'biocontainers/ivar:1.4.3--h43eeafb_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -43,4 +43,18 @@ process IVAR_CONSENSUS {
         ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def touch_mpileup = save_mpileup ? "touch ${prefix}.mpileup" : ''
+    """
+    touch ${prefix}.fa
+    touch ${prefix}.qual.txt
+    $touch_mpileup
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/ivar/consensus/tests/main.nf.test

@@ -0,0 +1,100 @@
+
+nextflow_process {
+
+    name "Test Process IVAR_CONSENSUS"
+    script "../main.nf"
+    process "IVAR_CONSENSUS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ivar"
+    tag "ivar/consensus"
+
+    test("test-ivar-consensus") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = false
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					process.out.fasta,
+					file(process.out.qual[0][1]).name, // empty
+					process.out.mpileup,
+					process.out.versions,
+                    file(process.out.versions[0]).readLines().collect { it.trim() } // Trap to catch conda version mismatches
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-ivar-consensus-mpileup") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = true
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					process.out.fasta,
+					file(process.out.qual[0][1]).name, // empty
+					file(process.out.mpileup[0][1]).name, // empty
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-ivar-consensus-mpileup-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = true
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/ivar/consensus/tests/main.nf.test.snap

@@ -0,0 +1,117 @@
+{
+    "test-ivar-consensus-mpileup-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.qual.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "mpileup": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "qual": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.qual.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T14:58:57.447441"
+    },
+    "test-ivar-consensus-mpileup": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.fa:md5,9e21a64818f4302b4dece5480fa5e8b8"
+                ]
+            ],
+            "test.qual.txt",
+            "test.mpileup",
+            [
+                "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T14:58:52.938906"
+    },
+    "test-ivar-consensus": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.fa:md5,9e21a64818f4302b4dece5480fa5e8b8"
+                ]
+            ],
+            "test.qual.txt",
+            [
+
+            ],
+            [
+                "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3"
+            ],
+            [
+                "\"IVAR_CONSENSUS\":",
+                "ivar: 1.4.3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T14:58:48.289344"
+    }
+}

modules/nf-core/ivar/consensus/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: IVAR_CONSENSUS {
+        ext.args2 = '-aa -A -d 0 -Q 0'
+    }
+}

tests/config/pytest_modules.yml

@@ -365,9 +365,6 @@ iphop/download:
 iphop/predict:
   - modules/nf-core/iphop/predict/**
   - tests/modules/nf-core/iphop/predict/**
-ivar/consensus:
-  - modules/nf-core/ivar/consensus/**
-  - tests/modules/nf-core/ivar/consensus/**
 ivar/variants:
   - modules/nf-core/ivar/variants/**
   - tests/modules/nf-core/ivar/variants/**