Add nf-test for biscuit/bsconv (#4493)

* Add nf-test for biscuit/bsconv * Add stub and stub test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
nf-core · May 7, 2024 · 606a549 · 606a549
1 parent 2a2b13f
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Showing 9 changed files with 161 additions and 58 deletions.
diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf
@@ -37,4 +37,20 @@ process BISCUIT_BSCONV {
         biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+    END_VERSIONS
+    """
+
+
 }
diff --git a/modules/nf-core/biscuit/bsconv/meta.yml b/modules/nf-core/biscuit/bsconv/meta.yml
@@ -29,7 +29,7 @@ input:
       type: file
       description: BAM file index
   - index:
-      type: dir
+      type: directory
       description: Biscuit genome index directory (generated with 'biscuit index')
       pattern: "BiscuitIndex"
 output:

diff --git a/modules/nf-core/biscuit/bsconv/tests/main.nf.test b/modules/nf-core/biscuit/bsconv/tests/main.nf.test
@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process BISCUIT_BSCONV"
+    script "../main.nf"
+    process "BISCUIT_BSCONV"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "biscuit"
+    tag "biscuit/bsconv"
+    tag "biscuit/index"
+
+
+    setup {
+        run("BISCUIT_INDEX") {
+            script "../../index/main.nf"
+            process {
+            """
+            input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            """
+            }
+        }
+    }
+
+    test("sarscov2-pe - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [id:'test', single_end:false ], // meta map
+                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+                            ]
+
+                input[1] = BISCUIT_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.bsconv_bam).match("bsconv_bam") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("sarscov2-pe - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [id:'test', single_end:false ], // meta map
+                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+                            ]
+
+                input[1] = BISCUIT_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/biscuit/bsconv/tests/main.nf.test.snap b/modules/nf-core/biscuit/bsconv/tests/main.nf.test.snap
@@ -0,0 +1,67 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,45455cc9522a3235fa482ad065a242b3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-07T15:28:04.601734997"
+    },
+    "sarscov2-pe - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,45455cc9522a3235fa482ad065a242b3"
+                ],
+                "bsconv_bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,45455cc9522a3235fa482ad065a242b3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-07T15:28:14.729945289"
+    },
+    "bsconv_bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,0d425851bd18963ebf1b6d727a7d02c7"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-07T15:28:04.580771449"
+    }
+}
diff --git a/modules/nf-core/biscuit/bsconv/tests/tags.yml b/modules/nf-core/biscuit/bsconv/tests/tags.yml
@@ -0,0 +1,2 @@
+biscuit/bsconv:
+  - "modules/nf-core/biscuit/bsconv/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -195,10 +195,6 @@ biscuit/biscuitblaster:
   - modules/nf-core/biscuit/index/**
   - modules/nf-core/biscuit/biscuitblaster/**
   - tests/modules/nf-core/biscuit/biscuitblaster/**
-biscuit/bsconv:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/bsconv/**
-  - tests/modules/nf-core/biscuit/bsconv/**
 biscuit/epiread:
   - modules/nf-core/biscuit/index/**
   - modules/nf-core/biscuit/epiread/**

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