Version bump

nf-core · Sep 6, 2024 · fe3aa92 · fe3aa92
1 parent d9b4429
commit fe3aa92
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Showing 4 changed files with 138 additions and 20 deletions.
diff --git a/modules/nf-core/gubbins/environment.yml b/modules/nf-core/gubbins/environment.yml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gubbins=3.0.0
+  - bioconda::gubbins=3.3.5
diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf
@@ -3,8 +3,8 @@ process GUBBINS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' :
-        'biocontainers/gubbins:3.0.0--py39h5bf99c6_0' }"
+        'https://depot.galaxyproject.org/singularity/gubbins:3.3.5--py39pl5321he4a0461_0' :
+        'biocontainers/gubbins:3.3.5--py39pl5321he4a0461_0' }"
 
     input:
     path alignment
@@ -27,6 +27,9 @@ process GUBBINS {
     script:
     def args = task.ext.args ?: ''
     """
+    mkdir numba_cache_dir
+    export NUMBA_CACHE_DIR='./numba_cache_dir'
+
     run_gubbins.py \\
         --threads $task.cpus \\
         $args \\
@@ -36,4 +39,26 @@ process GUBBINS {
         gubbins: \$(run_gubbins.py --version 2>&1)
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    mkdir numba_cache_dir
+    export NUMBA_CACHE_DIR='./numba_cache_dir'
+
+    touch ${alignment.baseName}.fasta
+    touch ${alignment.baseName}.gff
+    touch ${alignment.baseName}.vcf
+    touch ${alignment.baseName}.csv
+    touch ${alignment.baseName}.phylip
+    touch ${alignment.baseName}.recombination_predictions.embl
+    touch ${alignment.baseName}.branch_base_reconstruction.embl
+    touch ${alignment.baseName}.final_tree.tre
+    touch ${alignment.baseName}.node_labelled.final_tree.tre
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gubbins: \$(run_gubbins.py --version 2>&1)
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/gubbins/tests/main.nf.test b/modules/nf-core/gubbins/tests/main.nf.test
@@ -31,13 +31,33 @@ nextflow_process {
 					process.out.phylip,
 					file(process.out.embl_predicted[0]).name, // empty
 					process.out.embl_branch,
-					process.out.tree,
-					process.out.tree_labelled,
+					process.out.tree[0].collect { file(it).name }, // unstable
+					file(process.out.tree_labelled[0]).name,  // unstable
 					process.out.versions
 					).match()
 				}
             )
         }
     }
 
+    test("test-gubbins-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/gubbins/tests/main.nf.test.snap b/modules/nf-core/gubbins/tests/main.nf.test.snap
@@ -1,40 +1,113 @@
 {
+    "test-gubbins-stub": {
+        "content": [
+            {
+                "0": [
+                    "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "4": [
+                    "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "5": [
+                    "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "6": [
+                    "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "7": [
+                    [
+                        "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "9": [
+                    "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76"
+                ],
+                "embl_branch": [
+                    "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "embl_predicted": [
+                    "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "fasta": [
+                    "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "gff": [
+                    "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "phylip": [
+                    "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "stats": [
+                    "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "tree": [
+                    [
+                        "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tree_labelled": [
+                    "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "vcf": [
+                    "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T14:20:39.212181"
+    },
     "test-gubbins": {
         "content": [
             [
-                "all_sites.filtered_polymorphic_sites.fasta:md5,4cbfd93868d8ed7d4d8b099eba137134"
+                "all_sites.filtered_polymorphic_sites.fasta:md5,0f945512f071fd1599bb7455492e31bc"
             ],
             [
-                "all_sites.recombination_predictions.gff:md5,f95871e79968340cb82532e2c9b0c92b"
+                "all_sites.recombination_predictions.gff:md5,7605a21ad8812866adbdb5cada8a59d4"
             ],
-            "6e9a63f667f7facae3f3d3556618a9f6",
+            "d314daa06c635c0b31b132a1092ee4e3",
             [
-                "all_sites.per_branch_statistics.csv:md5,25e4fdb6681c3709a9add1d5632bbf3e"
+                "all_sites.per_branch_statistics.csv:md5,8012a76a2486a8b3dfe78d6902b56ed4"
             ],
             [
-                "all_sites.filtered_polymorphic_sites.phylip:md5,0a77f397a7797c5c3386832745b0c97a"
+                "all_sites.filtered_polymorphic_sites.phylip:md5,d28da2dd14d08bbb996756064516aee1"
             ],
             "all_sites.recombination_predictions.embl",
             [
-                "all_sites.branch_base_reconstruction.embl:md5,9e051646d630f528fff58f1f73286006"
-            ],
-            [
-                [
-                    "all_sites.final_tree.tre:md5,095689c565948a634c654fa4f28542d9",
-                    "all_sites.node_labelled.final_tree.tre:md5,c16333d8b1c0502a7cd09e6531459f9f"
-                ]
+                "all_sites.branch_base_reconstruction.embl:md5,9dfd7e411404360ce4a7938aab8db701"
             ],
             [
-                "all_sites.node_labelled.final_tree.tre:md5,c16333d8b1c0502a7cd09e6531459f9f"
+                "all_sites.final_tree.tre",
+                "all_sites.node_labelled.final_tree.tre"
             ],
+            "all_sites.node_labelled.final_tree.tre",
             [
-                "versions.yml:md5,5b1fc0a22fc6b4c4460858b2f478c937"
+                "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-06T08:59:35.386435"
+        "timestamp": "2024-09-06T14:16:35.669362"
     }
 }