Merge pull request nf-core#1232 from maxulysse/star_igenomes

Adding tests for star_align igenomes
maxulysse · Mar 5, 2024 · 4ef4025 · 4ef4025
2 parents 34e51dd + 4d9e2fb
commit 4ef4025
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Showing 4 changed files with 188 additions and 2 deletions.
diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf
@@ -22,14 +22,15 @@ process STAR_GENOMEGENERATE_IGENOMES {
     def args = task.ext.args ?: ''
     def args_list = args.tokenize()
     def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    def include_gtf = gtf ? "--sjdbGTFfile $gtf" : ''
     if (args_list.contains('--genomeSAindexNbases')) {
         """
         mkdir star
         STAR \\
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             $memory \\
             $args
@@ -51,7 +52,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             --genomeSAindexNbases \$NUM_BASES \\
             $memory \\

diff --git a/modules/local/star_genomegenerate_igenomes/tests/main.nf.test b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test
@@ -0,0 +1,93 @@
+nextflow_process {
+
+    name "Test Process STAR_GENOMEGENERATE_IGENOMES"
+    script "../main.nf"
+    process "STAR_GENOMEGENERATE_IGENOMES"
+
+    tag "STAR_GENOMEGENERATE_IGENOMES"
+
+    test("fasta with gtf") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") },
+                { assert snapshot(process.out.versions).match("fasta_gtf_versions") }
+            )
+        }
+    }
+
+    test("fasta with gtf - stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") },
+                { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") }
+            )
+        }
+    }
+
+    test("fasta no gtf") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([ ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") },
+                { assert snapshot(process.out.versions).match("fasta_versions") }
+            )
+        }
+
+    }
+
+    test("fasta no gtf - stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([ ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") },
+                { assert snapshot(process.out.versions).match("fasta_stub_versions") }
+            )
+        }
+    }
+}
diff --git a/modules/local/star_genomegenerate_igenomes/tests/main.nf.test.snap b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test.snap
@@ -0,0 +1,90 @@
+{
+    "fasta_gtf_versions": {
+        "content": [
+            [
+                "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:28:05.069709"
+    },
+    "fasta_stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:31:12.153651"
+    },
+    "fasta_gtf_stub_index": {
+        "content": [
+            "[]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:28:16.309869"
+    },
+    "fasta_gtf_stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:28:16.337298"
+    },
+    "fasta_index": {
+        "content": [
+            "[]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:30:56.504744"
+    },
+    "fasta_versions": {
+        "content": [
+            [
+                "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:30:56.575367"
+    },
+    "fasta_gtf_index": {
+        "content": [
+            "[]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:28:05.031195"
+    },
+    "fasta_stub_index": {
+        "content": [
+            "[]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-05T10:31:12.12097"
+    }
+}
diff --git a/modules/local/star_genomegenerate_igenomes/tests/tags.yml b/modules/local/star_genomegenerate_igenomes/tests/tags.yml
@@ -0,0 +1,2 @@
+STAR_GENOMEGENERATE_IGENOMES:
+  - modules/local/star_genomegenerate_igenomes/**