sourmash/compare stub, nf-test, snapshot

modules/nf-core/sourmash/compare/main.nf

@@ -14,21 +14,22 @@ process SOURMASH_COMPARE {
     val save_csv
 
     output:
-    tuple val(meta), path("*comp.npy.labels.txt"), path("*comp.npy"), optional:true, emit: matrix
-    path "*comp.csv"       , optional:true, emit: csv
-    path "versions.yml"    , emit: versions
+    tuple val(meta), path("*comp.npy")            , emit: matrix, optional:true
+    tuple val(meta), path("*comp.npy.labels.txt") , emit: labels, optional:true
+    tuple val(meta), path("*comp.csv")            , emit: csv   , optional:true
+    path "versions.yml"                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args   = task.ext.args     ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix   ?: "${meta.id}"
     def comp   = save_numpy_matrix ? "--output comp.npy"  : ''
     def csv    = save_csv          ? "--csv comp.csv" : ''
     if ( !save_numpy_matrix && !save_csv ) error "Supply either save_numpy_matrix, save_csv, or both or no output will be created"
     def ffile = file_list ? "--from-file ${file_list}" : ''
-    def sigs = signatures ? "${signatures.join(' ')}" : ''
+    def sigs = signatures ? "${signatures.sort{it.toString()}.join(' ')}" : ''
     if ( !file_list && !signatures ) error "Supply either signatures, file_list, or both"
     """
     sourmash compare \\
@@ -44,4 +45,16 @@ process SOURMASH_COMPARE {
         sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch comp.npy.labels.txt
+    touch comp.npy
+    touch comp.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
+    END_VERSIONS
+    """
 }

modules/nf-core/sourmash/compare/meta.yml

@@ -15,7 +15,7 @@ tools:
       documentation: "https://sourmash.readthedocs.io/"
       tool_dev_url: "https://github.com/sourmash-bio/sourmash"
       doi: "10.21105/joss.00027"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
@@ -50,7 +50,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - numpy_matrix:
+  - matrix:
       type: file
       description: An optional (dis)similarity matrix numpy binary format
       pattern: "*.comp"

modules/nf-core/sourmash/compare/tests/main.nf.test

@@ -0,0 +1,81 @@
+nextflow_process {
+
+    name "Test Process SOURMASH_COMPARE"
+    script "../main.nf"
+    process "SOURMASH_COMPARE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sourmash"
+    tag "sourmash/compare"
+    tag "sourmash/sketch"
+
+    setup {
+        run("SOURMASH_SKETCH") {
+            script "../../sketch/main.nf"
+            process {
+            """
+            input[0] = Channel.fromList([
+                        [
+                            [ id: 'test1' ],
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ],
+                        [
+                            [ id: 'test2' ],
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ]
+                ]
+            )
+            """
+            }
+        }
+    }
+
+    test("sarscov2 genome [fasta]") {
+
+        when {
+            process {
+                """
+                input[0] = SOURMASH_SKETCH.out.signatures.collect{ it[1] }.map { it -> [ [id: "group1" ], it ] }
+                input[1] = []
+                input[2] = true // save_numpy_matrix
+                input[3] = true // save_csv
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = SOURMASH_SKETCH.out.signatures.collect{ it[1] }.map { it -> [ [id: "group1" ], it ] }
+                input[1] = []
+                input[2] = true // save_numpy_matrix
+                input[3] = true // save_csv
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/sourmash/compare/tests/main.nf.test.snap

@@ -0,0 +1,132 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy.labels.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,6c61aed52902d1e343640d606122f411"
+                ],
+                "csv": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "labels": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy.labels.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "matrix": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6c61aed52902d1e343640d606122f411"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T14:45:34.007399207"
+    },
+    "sarscov2 genome [fasta]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy:md5,8a8683e1201544f28e2c2e21d2b89e4f"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy.labels.txt:md5,5bdd30886cf6f00a7286ac6e7322a46e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.csv:md5,79bb8895742bfa32d4a39d2fbc2be941"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,6c61aed52902d1e343640d606122f411"
+                ],
+                "csv": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.csv:md5,79bb8895742bfa32d4a39d2fbc2be941"
+                    ]
+                ],
+                "labels": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy.labels.txt:md5,5bdd30886cf6f00a7286ac6e7322a46e"
+                    ]
+                ],
+                "matrix": [
+                    [
+                        {
+                            "id": "group1"
+                        },
+                        "comp.npy:md5,8a8683e1201544f28e2c2e21d2b89e4f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6c61aed52902d1e343640d606122f411"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T14:45:19.227025783"
+    }
+}

modules/nf-core/sourmash/compare/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName:SOURMASH_COMPARE {
+        ext.args = "--ksize 31"
+     }
+}

modules/nf-core/sourmash/compare/tests/tags.yml

@@ -0,0 +1,2 @@
+sourmash/compare:
+  - "modules/nf-core/sourmash/compare/**"

tests/config/pytest_modules.yml

@@ -1566,9 +1566,6 @@ snpsift/split:
 somalier/ancestry:
   - modules/nf-core/somalier/ancestry/**
   - tests/modules/nf-core/somalier/ancestry/**
-sourmash/compare:
-  - modules/nf-core/sourmash/compare/**
-  - tests/modules/nf-core/sourmash/compare/**
 sourmash/gather:
   - modules/nf-core/sourmash/gather/**
   - tests/modules/nf-core/sourmash/gather/**