mmseqs version bump - cluster (+tests ported to nf-test), createdb, c…

…reatetsv, databases, linclust (#7170) * mmseqs version bump - cluster, createdb, createtsv, databases, linclsut * removed tags.yml files
nf-core · Dec 6, 2024 · a437c79 · a437c79
1 parent 51ae540
commit a437c79
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Showing 24 changed files with 137 additions and 102 deletions.
diff --git a/modules/nf-core/mmseqs/cluster/environment.yml b/modules/nf-core/mmseqs/cluster/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=15.6f452
+  - bioconda::mmseqs2=16.747c6
diff --git a/modules/nf-core/mmseqs/cluster/main.nf b/modules/nf-core/mmseqs/cluster/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_CLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
+        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
 
     input:
     tuple val(meta), path(db_input)

diff --git a/modules/nf-core/mmseqs/cluster/tests/main.nf.test b/modules/nf-core/mmseqs/cluster/tests/main.nf.test
@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process MMSEQS_CLUSTER"
+    script "../main.nf"
+    process "MMSEQS_CLUSTER"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mmseqs"
+    tag "mmseqs/cluster"
+    tag "untar"
+
+    test("Should cluster an mmseqs database") {
+
+        setup {
+            run("UNTAR") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/mmseqs.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.db_cluster.size() == 1 },
+                {
+                    def all_files = file(process.out.db_cluster[0][1]).listFiles()
+                    def all_file_names = all_files.collect { it.name }.toSorted()
+                    def stable_file_names = [
+                        'test_output_cluster.dbtype',
+                        'test_output_cluster.index'
+                    ]
+                    def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted()
+
+                    assert snapshot(
+                        all_file_names,
+                        stable_files,
+                        process.out.versions[0]
+                    ).match()
+                }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap b/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap
@@ -0,0 +1,22 @@
+{
+    "Should cluster an mmseqs database": {
+        "content": [
+            [
+                "test_output_cluster.0",
+                "test_output_cluster.1",
+                "test_output_cluster.dbtype",
+                "test_output_cluster.index"
+            ],
+            [
+                "test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089",
+                "test_output_cluster.index:md5,ca7e1f0967222b06d7e05e47bcbe1e50"
+            ],
+            "versions.yml:md5,4acad55952c6d1fb41ad7f5a44468aed"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-05T10:44:45.713270981"
+    }
+}
diff --git a/...es/nf-core/mmseqs/cluster/nextflow.config → ...core/mmseqs/cluster/tests/nextflow.config b/...es/nf-core/mmseqs/cluster/nextflow.config → ...core/mmseqs/cluster/tests/nextflow.config
@@ -1,7 +1,4 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: UNTAR {
         publishDir = [ enabled : false ]
     }
@@ -10,5 +7,4 @@ process {
         ext.prefix = "test_output_cluster"
         ext.args = '--remove-tmp-files 1 -v 3 '
     }
-
 }
diff --git a/modules/nf-core/mmseqs/createdb/environment.yml b/modules/nf-core/mmseqs/createdb/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=15.6f452
+  - bioconda::mmseqs2=16.747c6
diff --git a/modules/nf-core/mmseqs/createdb/main.nf b/modules/nf-core/mmseqs/createdb/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_CREATEDB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
+        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
 
     input:
     tuple val(meta), path(sequence)

diff --git a/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap
@@ -20,14 +20,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,e644cbe263d4560298438a24f268eb6f"
+                "versions.yml:md5,d30a1af41e7f3f5b67afdec412fa693f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-08-09T10:01:44.163384"
+        "timestamp": "2024-12-05T10:35:27.322864475"
     },
     "Should build an mmseqs db from a zipped amino acid sequence file": {
         "content": [
@@ -49,13 +49,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,e644cbe263d4560298438a24f268eb6f"
+                "versions.yml:md5,d30a1af41e7f3f5b67afdec412fa693f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-08-09T10:01:48.894044"
+        "timestamp": "2024-12-05T10:35:33.418552595"
     }
 }
diff --git a/modules/nf-core/mmseqs/createdb/tests/tags.yml b/modules/nf-core/mmseqs/createdb/tests/tags.yml
diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=15.6f452
+  - bioconda::mmseqs2=16.747c6
diff --git a/modules/nf-core/mmseqs/createtsv/main.nf b/modules/nf-core/mmseqs/createtsv/main.nf
@@ -5,8 +5,8 @@ process MMSEQS_CREATETSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
+        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
 
     input:
     tuple val(meta), path(db_result)

diff --git a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ],
                 "tsv": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-07-12T13:55:17.642787"
+        "timestamp": "2024-12-05T10:50:48.386202112"
     },
     "mmseqs/createtsv - sarscov2 - cluster - stub": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ],
                 "tsv": [
                     [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-07-12T13:55:33.645454"
+        "timestamp": "2024-12-05T10:50:56.33475153"
     },
     "mmseqs/createtsv - bacteroides_fragilis - taxonomy": {
         "content": [
@@ -82,7 +82,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ],
                 "tsv": [
                     [
@@ -94,15 +94,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-07-12T13:54:45.718678"
+        "timestamp": "2024-12-05T11:25:54.741775111"
     },
     "mmseqs/createtsv - sarscov2 - cluster": {
         "content": [
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ],
                 "tsv": [
                     [
@@ -129,14 +129,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f"
+                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-07-12T13:55:02.731974"
+        "timestamp": "2024-12-05T10:50:42.432284995"
     }
 }
diff --git a/modules/nf-core/mmseqs/createtsv/tests/tags.yml b/modules/nf-core/mmseqs/createtsv/tests/tags.yml
diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=15.6f452
+  - bioconda::mmseqs2=16.747c6
diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_DATABASES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
+        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
 
     input:
     val database

diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap
@@ -15,14 +15,14 @@
                 "database_taxonomy"
             ],
             [
-                "versions.yml:md5,b038db45e5934b8f0f743449bbac01b4"
+                "versions.yml:md5,e236ec16fdc9f054d0a660d02e680255"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-09-06T15:43:58.454012"
+        "timestamp": "2024-12-05T14:33:16.697954954"
     },
     "test-mmseqs-databases-stub": {
         "content": [

diff --git a/modules/nf-core/mmseqs/linclust/environment.yml b/modules/nf-core/mmseqs/linclust/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=15.6f452
+  - bioconda::mmseqs2=16.747c6
diff --git a/modules/nf-core/mmseqs/linclust/main.nf b/modules/nf-core/mmseqs/linclust/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_LINCLUST {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
+        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
 
     input:
     tuple val(meta), path(db_input)

diff --git a/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap b/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap
@@ -11,12 +11,12 @@
                 "test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089",
                 "test_output_cluster.index:md5,38908275cdd5727ae0eb9be017f9ca13"
             ],
-            "versions.yml:md5,65ce4e8b36259f881d11b0d8caaee69a"
+            "versions.yml:md5,969cb26241f66ac758c104f9561860b1"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-08-13T10:40:19.482219"
+        "timestamp": "2024-12-05T10:43:26.020522437"
     }
 }
diff --git a/modules/nf-core/mmseqs/linclust/tests/tags.yml b/modules/nf-core/mmseqs/linclust/tests/tags.yml