stubs and test for rnaseq modules - part IV (#5939)

* fix stubs and add stub tests * fix linting * fix some linting * fix linting * better comment * change container * update snapshots * improve untar stubs * update snapshots * update snapshots * update env * better * use seqera containers * quay.io * proper usage * update snapshots * keep ubuntu for now * update tests and snap * update test and snapshot * update test and snapshot
nf-core · Jul 12, 2024 · 4e5f468 · 4e5f468
1 parent 0554167
commit 4e5f468
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Showing 45 changed files with 652 additions and 293 deletions.
diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap
@@ -294,8 +294,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-02-09T17:06:15.671842533"
+        "timestamp": "2024-07-11T16:35:51.079804"
     }
 }
diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test
@@ -10,46 +10,47 @@ nextflow_process {
     tag "antismash/antismashlitedownloaddatabases"
     tag "untar"
 
-    setup {
+    test("antiSMASH-lite downloaddatabases") {
 
-        run("UNTAR", alias: "UNTAR_CSS") {
-            script "modules/nf-core/untar/main.nf"
-            process {
-            """
-            input[0] = [
-                [ ],
-                file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
-            ]
-            """
+        setup {
+
+            run("UNTAR", alias: "UNTAR_CSS") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                """
+                input[0] = [
+                    [ ],
+                    file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+                ]
+                """
+                }
             }
-        }
 
-        run("UNTAR", alias: "UNTAR_DETECTION") {
-            script "modules/nf-core/untar/main.nf"
-            process {
-            """
-            input[0] = [
-                [ ],
-                file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
-            ]
-            """
+            run("UNTAR", alias: "UNTAR_DETECTION") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                """
+                input[0] = [
+                    [ ],
+                    file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+                ]
+                """
+                }
             }
-        }
 
-        run("UNTAR", alias: "UNTAR_MODULES") {
-            script "modules/nf-core/untar/main.nf"
-            process {
-            """
-            input[0] = [
-                [ ],
-                file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
-            ]
-            """
+            run("UNTAR", alias: "UNTAR_MODULES") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                """
+                input[0] = [
+                    [ ],
+                    file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+                ]
+                """
+                }
             }
         }
-    }
 
-test("antiSMASH-lite downloaddatabases") {
         when {
             process {
                 """
@@ -64,18 +65,56 @@ test("antiSMASH-lite downloaddatabases") {
             assertAll(
                 { assert process.success },
                 { assert snapshot (
-                     file(process.out.database.get(0)).list().sort(),
-                     process.out.versions,
+                    file(process.out.database.get(0)).list().sort(),
+                    process.out.versions,
                 ).match() }
             )
         }
-
     }
 
     test("antiSMASH-lite downloaddatabases - stub") {
 
         options "-stub"
 
+        setup {
+
+            run("UNTAR", alias: "UNTAR_CSS") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                """
+                input[0] = [
+                    [ ],
+                    file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+                ]
+                """
+                }
+            }
+
+            run("UNTAR", alias: "UNTAR_DETECTION") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                """
+                input[0] = [
+                    [ ],
+                    file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+                ]
+                """
+                }
+            }
+
+            run("UNTAR", alias: "UNTAR_MODULES") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                """
+                input[0] = [
+                    [ ],
+                    file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+                ]
+                """
+                }
+            }
+        }
+
         when {
             process {
                 """
@@ -92,7 +131,5 @@ test("antiSMASH-lite downloaddatabases") {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap
@@ -32,9 +32,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-02-07T23:13:12.85814463"
+        "timestamp": "2024-07-12T13:41:29.456143"
     },
     "antiSMASH-lite downloaddatabases": {
         "content": [
@@ -55,8 +55,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-02-07T23:12:29.947339678"
+        "timestamp": "2024-07-12T13:41:08.116244"
     }
 }
diff --git a/modules/nf-core/bracken/build/tests/main.nf.test b/modules/nf-core/bracken/build/tests/main.nf.test
@@ -10,18 +10,18 @@ nextflow_process {
     tag "bracken/build"
     tag "untar"
 
-    setup {
-        run ("UNTAR") {
-            script "../../../untar/main.nf"
-            process {
-                """
-                input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)]
-                """
+    test("kraken2 - db") {
+
+        setup {
+            run ("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)]
+                    """
+                }
             }
         }
-    }
-
-    test("kraken2 - db") {
 
         when {
             process {
@@ -41,6 +41,7 @@ nextflow_process {
                         file("${process.out.bracken_files[0][1]}/database100mers.kmer_distrib").name,
                         file("${process.out.bracken_files[0][1]}/database100mers.kraken").name,
                         file("${process.out.bracken_files[0][1]}/database.kraken").name,
+                        process.out.versions
                     ).match()
                 }
             )
@@ -52,6 +53,17 @@ nextflow_process {
 
         options "-stub"
 
+        setup {
+            run ("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)]
+                    """
+                }
+            }
+        }
+
         when {
             process {
                 """
@@ -66,7 +78,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/bracken/build/tests/main.nf.test.snap b/modules/nf-core/bracken/build/tests/main.nf.test.snap
@@ -6,13 +6,16 @@
             "database.kraken",
             "database100mers.kmer_distrib",
             "database100mers.kraken",
-            "database.kraken"
+            "database.kraken",
+            [
+                "versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b"
+            ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-04-17T18:41:03.693430543"
+        "timestamp": "2024-07-12T13:45:17.37462"
     },
     "kraken2 - db - stub": {
         "content": [
@@ -26,7 +29,28 @@
                             "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            [
+                                [
+                                    "G46z5ZvKEd.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "G46z5ZvKEd.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "prelim_map_MtGz4nUfR3.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "prelim_map_eNakvrOVZm.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "z_4A5lulyr.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "z_4A5lulyr.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ]
+                            ],
+                            "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            [
+                                "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                         ]
                     ]
                 ],
@@ -66,7 +90,28 @@
                             "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            [
+                                [
+                                    "G46z5ZvKEd.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "G46z5ZvKEd.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "prelim_map_MtGz4nUfR3.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "prelim_map_eNakvrOVZm.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "z_4A5lulyr.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "z_4A5lulyr.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ]
+                            ],
+                            "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            [
+                                "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                         ]
                     ]
                 ],
@@ -77,8 +122,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-04-17T18:41:14.406736156"
+        "timestamp": "2024-07-12T13:45:26.452181"
     }
 }
diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test
@@ -42,10 +42,10 @@ nextflow_process {
                     file(process.out.results[0][1]).name,
                     file(process.out.fastq_mapped[0][1][0]).name,
                     file(process.out.fastq_unmapped[0][1][0]).name,
+                    process.out.versions
                 ).match() }
             )
         }
-
     }
 
     test("sarscov2_fastq_pe") {
@@ -56,8 +56,8 @@ nextflow_process {
                 input[0] = [
                                 [ id:'test', single_end:false ], // meta map
                                 [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                                  file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-                           ]
+                                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+                        ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
                 input[2] = true
                 input[3] = true
@@ -73,10 +73,10 @@ nextflow_process {
                     file(process.out.results[0][1]).name,
                     file(process.out.fastq_mapped[0][1][0]).name,
                     file(process.out.fastq_unmapped[0][1][0]).name,
+                    process.out.versions
                 ).match() }
             )
         }
-
     }
 
     test("sarscov2_fastq_se_stub") {
@@ -100,7 +100,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }