Added nf-test for bbmap/sendsketch (#6335)

modules/nf-core/bbmap/sendsketch/meta.yml

@@ -12,7 +12,7 @@ tools:
       description: "BBMap is a short read aligner, as well as various other bioinformatic tools."
       homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
       documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
-      licence: "['UC-LBL license (see package)']"
+      licence: ["UC-LBL license (see package)"]
 input:
   - meta:
       type: map
@@ -34,7 +34,7 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - hits:
-      type: txt
+      type: file
       description: .txt file containing hits from a query seuqnce to various reference sequences output
       pattern: "*.{txt}"
 authors:

modules/nf-core/bbmap/sendsketch/tests/main.nf.test

@@ -0,0 +1,70 @@
+
+nextflow_process {
+
+    name "Test Process BBMAP_SENDSKETCH"
+    script "../main.nf"
+    process "BBMAP_SENDSKETCH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bbmap"
+    tag "bbmap/sendsketch"
+
+    test("test-bbmap-sendsketch-single") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				    ]
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.hits[0][1]).readLines()[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-bbmap-sendsketch-paired") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)
+                    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.hits[0][1]).readLines()[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap

@@ -0,0 +1,40 @@
+{
+    "test-bbmap-sendsketch-paired": {
+        "content": [
+            [
+                "0.52%\t0.14%\t82.66%\t.\t26.68%\t1.03%\t60\t10\t9534\t30656K\t46\tChlorocebus aethiops",
+                "0.46%\t0.12%\t82.30%\t.\t26.38%\t1.10%\t53\t7\t33548\t30986K\t46\tColobus guereza",
+                "9.02%\t0.03%\t91.56%\t.\t0.34%\t1.88%\t48\t8\t9606\t2387M\t26130\tHomo sapiens",
+                "0.30%\t0.08%\t80.90%\t.\t27.42%\t1.23%\t35\t8\t9523\t29749K\t44\tPlecturocebus moloch",
+                "6.70%\t0.02%\t90.53%\t.\t0.34%\t4.10%\t36\t0\t9595\t2355M\t5730\tGorilla gorilla gorilla"
+            ],
+            [
+                "versions.yml:md5,694697087b868316aa450d1bc3775373"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:29:22.985067"
+    },
+    "test-bbmap-sendsketch-single": {
+        "content": [
+            [
+                "0.66%\t0.53%\t83.30%\t.\t80.66%\t0.56%\t20\t17\t9593\t47555\t9\tGorilla gorilla",
+                "0.14%\t0.07%\t78.52%\t.\t48.11%\t1.09%\t4\t4\t27679\t78571\t4\tSaimiri boliviensis",
+                "7.69%\t0.01%\t90.45%\t.\t0.12%\t3.85%\t4\t1\t9534\t30656K\t46\tChlorocebus aethiops",
+                "0.17%\t0.04%\t79.27%\t.\t23.69%\t1.26%\t3\t1\t67082\t158942\t1\tBeAn 58058 virus",
+                "5.56%\t0.01%\t89.72%\t.\t0.12%\t5.56%\t3\t0\t9523\t29749K\t44\tPlecturocebus moloch"
+            ],
+            [
+                "versions.yml:md5,694697087b868316aa450d1bc3775373"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:29:03.529673"
+    }
+}

tests/config/pytest_modules.yml

@@ -58,9 +58,6 @@ bbmap/index:
 bbmap/pileup:
   - modules/nf-core/bbmap/pileup/**
   - tests/modules/nf-core/bbmap/pileup/**
-bbmap/sendsketch:
-  - modules/nf-core/bbmap/sendsketch/**
-  - tests/modules/nf-core/bbmap/sendsketch/**
 bcftools/convert:
   - modules/nf-core/bcftools/convert/**
   - tests/modules/nf-core/bcftools/convert/**