added stub section and tests for bcstools_consensus

DimitriTernovoj · Aug 20, 2024 · 10b48f5 · 10b48f5
1 parent a16e02e
commit 10b48f5
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diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf
@@ -8,7 +8,7 @@ process BCFTOOLS_CONSENSUS {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(tbi), path(fasta)
+    tuple val(meta), path(vcf), path(tbi), path(fasta), path(mask)
 
     output:
     tuple val(meta), path('*.fa'), emit: fasta
@@ -20,12 +20,14 @@ process BCFTOOLS_CONSENSUS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def masking = mask ? "-m $mask" : ""
     """
     cat $fasta \\
         | bcftools \\
             consensus \\
             $vcf \\
             $args \\
+            $masking \\
             > ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/bcftools/consensus/meta.yml b/modules/nf-core/bcftools/consensus/meta.yml
@@ -30,6 +30,10 @@ input:
       type: file
       description: FASTA reference file
       pattern: "*.{fasta,fa}"
+  - mask:
+      type: file
+      description: BED file used for masking
+      pattern: "*.{bed}"
 output:
   - meta:
       type: map

diff --git a/modules/nf-core/bcftools/consensus/tests/main.nf.test b/modules/nf-core/bcftools/consensus/tests/main.nf.test
@@ -0,0 +1,90 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_CONSENSUS"
+    script "../main.nf"
+    process "BCFTOOLS_CONSENSUS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/consensus"
+
+    test("bcftools - test") {
+
+        tag "bcftools_consensus"
+
+        when {
+            process{
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            ) 
+        }
+    }
+
+    test("bcftools - test - no mask") {
+
+        tag "bcftools_consensus"
+
+        when {
+            process{
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            ) 
+        }
+    }
+
+    test("bcftools - stub - test") {
+
+        tag "stub"
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()}
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/bcftools/consensus/tests/main.nf.test.snap b/modules/nf-core/bcftools/consensus/tests/main.nf.test.snap
@@ -0,0 +1,101 @@
+{
+    "bcftools - stub - test": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,313f4a657187fdaf293c4ed69d98c112"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,313f4a657187fdaf293c4ed69d98c112"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-08-20T11:07:44.650952324"
+    },
+    "bcftools - test": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,313f4a657187fdaf293c4ed69d98c112"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,313f4a657187fdaf293c4ed69d98c112"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-08-20T11:07:31.213119374"
+    },
+    "bcftools - test - no mask": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,e57d3e4d113f989bc069c5fd61627091"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,e57d3e4d113f989bc069c5fd61627091"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-08-20T11:07:38.238225252"
+    }
+}