From 104bb763c82e18cc3768abed10b251ebba321c0e Mon Sep 17 00:00:00 2001
From: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Date: Tue, 7 Jan 2025 09:30:49 +0100
Subject: [PATCH 1/4] Add missing file input to bcftools/annotate (#6942)

Add input to bcftools/annotate
---
 modules/nf-core/bcftools/annotate/main.nf     |   3 +
 modules/nf-core/bcftools/annotate/meta.yml    |   3 +
 .../bcftools/annotate/tests/main.nf.test      |  67 +++-
 .../bcftools/annotate/tests/main.nf.test.snap | 315 ++++++++++--------
 4 files changed, 231 insertions(+), 157 deletions(-)

diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf
index 9ffdfdf0a49..b6b73309b89 100644
--- a/modules/nf-core/bcftools/annotate/main.nf
+++ b/modules/nf-core/bcftools/annotate/main.nf
@@ -10,6 +10,7 @@ process BCFTOOLS_ANNOTATE {
     input:
     tuple val(meta), path(input), path(index), path(annotations), path(annotations_index)
     path(header_lines)
+    path(rename_chrs)
 
     output:
     tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
@@ -25,6 +26,7 @@ process BCFTOOLS_ANNOTATE {
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def header_file = header_lines ? "--header-lines ${header_lines}" : ''
     def annotations_file = annotations ? "--annotations ${annotations}" : ''
+    def rename_chrs_file = rename_chrs ? "--rename-chrs ${rename_chrs}" : ''
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                     args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
                     args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
@@ -40,6 +42,7 @@ process BCFTOOLS_ANNOTATE {
         annotate \\
         $args \\
         $annotations_file \\
+        $rename_chrs_file \\
         $header_file \\
         --output ${prefix}.${extension} \\
         --threads $task.cpus \\
diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml
index 5bfccd2bd8f..fd2c91c706a 100644
--- a/modules/nf-core/bcftools/annotate/meta.yml
+++ b/modules/nf-core/bcftools/annotate/meta.yml
@@ -35,6 +35,9 @@ input:
   - - header_lines:
         type: file
         description: Contains lines to append to the output VCF header
+  - - rename_chrs:
+        type: file
+        description: Rename annotations according to this file containing "old_name new_name\n" pairs separated by whitespaces, each on a separate line.
 output:
   - vcf:
       - meta:
diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test
index 3a5c493314f..fd6d2cd37f6 100644
--- a/modules/nf-core/bcftools/annotate/tests/main.nf.test
+++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test
@@ -9,7 +9,7 @@ nextflow_process {
     tag "bcftools"
     tag "bcftools/annotate"
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output") {
 
         config "./vcf.config"
 
@@ -24,6 +24,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -40,7 +41,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") {
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output") {
 
         config "./vcf.config"
 
@@ -55,6 +56,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -70,7 +72,7 @@ nextflow_process {
         }
 
     }
-        test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") {
+        test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index") {
 
         config "./vcf_gz_index.config"
 
@@ -85,6 +87,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -104,7 +107,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi") {
 
         config "./vcf_gz_index_csi.config"
 
@@ -119,6 +122,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -138,7 +142,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi") {
 
         config "./vcf_gz_index_tbi.config"
 
@@ -153,6 +157,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -171,7 +176,8 @@ nextflow_process {
         }
 
     }
-    test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") {
+
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], header, [] - bcf_output") {
 
         config "./bcf.config"
 
@@ -189,6 +195,7 @@ nextflow_process {
                     '##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">',
                     '##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">'
                 ).collectFile(name:"headers.vcf", newLine:true)
+                input[2] = []
                 """
             }
         }
@@ -205,7 +212,43 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") {
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index") {
+
+        config "./vcf_gz_index.config"
+ 
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = Channel.of(
+                    '##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">',
+                    '##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">'
+                ).collectFile(name:"headers.vcf", newLine:true)
+                input[2] = Channel.of('MT192765.1 renamed').collectFile(name:"rename.txt", newLine:true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).LinesGzip.contains("##contig=<ID=renamed,length=29829>")},
+                { assert snapshot(
+                    process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub") {
 
         config "./vcf.config"
         options "-stub"
@@ -221,6 +264,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -234,7 +278,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub") {
 
         config "./vcf_gz_index.config"
         options "-stub"
@@ -250,6 +294,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -264,7 +309,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub") {
 
         config "./vcf_gz_index_csi.config"
         options "-stub"
@@ -280,6 +325,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
@@ -294,7 +340,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub") {
 
         config "./vcf_gz_index_tbi.config"
         options "-stub"
@@ -310,6 +356,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
+                input[2] = []
                 """
             }
         }
diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
index bac2224a3b5..16828b6ce04 100644
--- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
@@ -1,4 +1,37 @@
 {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.tbi"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T14:02:05.809043894"
+    },
     "bcf": {
         "content": [
             [
@@ -20,7 +53,7 @@
         },
         "timestamp": "2024-06-12T16:39:33.331888"
     },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": {
+    "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output": {
         "content": [
             [
                 [
@@ -32,15 +65,24 @@
                 ]
             ],
             [
-                
-            ],
+                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T14:01:32.326248064"
+    },
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output": {
+        "content": [
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test_vcf.vcf.gz.csi"
+                    "test_vcf.vcf.gz"
                 ]
             ],
             [
@@ -48,12 +90,12 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-15T10:07:59.658031137"
+        "timestamp": "2024-11-06T14:01:17.821142466"
     },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub": {
         "content": [
             {
                 "0": [
@@ -66,31 +108,31 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "2": [
+                    
                 ],
                 "3": [
                     "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
                 ],
                 "csi": [
+                    
+                ],
+                "tbi": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "tbi": [
-                    
                 ],
                 "vcf": [
                     [
@@ -107,45 +149,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-15T10:09:05.096883418"
+        "timestamp": "2024-11-06T14:03:12.574479421"
     },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz.csi"
-                ]
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-08-15T10:08:10.581301219"
-    },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub": {
         "content": [
             {
                 "0": [
@@ -187,87 +196,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-08-15T10:08:43.975017625"
-    },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz.tbi"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-15T10:08:21.354059092"
+        "timestamp": "2024-11-06T14:02:38.89910979"
     },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz"
-                ]
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-08-15T10:07:37.788393317"
-    },
-    "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz"
-                ]
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-08-15T10:07:48.500746325"
-    },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub": {
         "content": [
             {
                 "0": [
@@ -280,31 +214,31 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "2": [
-                    
                 ],
                 "3": [
                     "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
                 ],
                 "csi": [
-                    
-                ],
-                "tbi": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "tbi": [
+                    
                 ],
                 "vcf": [
                     [
@@ -321,12 +255,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-15T10:09:16.094918834"
+        "timestamp": "2024-11-06T14:02:49.803045339"
     },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub": {
         "content": [
             {
                 "0": [
@@ -380,9 +314,96 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T14:03:00.654715777"
+    },
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T14:01:45.446114465"
+    },
+    "sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz"
+                ]
+            ],
+            [
+                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T13:58:14.280394724"
+    },
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-15T10:08:54.366358502"
+        "timestamp": "2024-11-06T14:01:55.70445216"
     }
 }
\ No newline at end of file

From 09681763f3d9c772b26599d75b669957a04b1d33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Tue, 7 Jan 2025 17:16:53 +0100
Subject: [PATCH 2/4] Fix docker ownserhip issue and remove userEmulation
 (#7272)

* fix docker ownership issue

* remove deprecated docker.userEmulation

* add stub test

* move setup step to beginning of process

* remove stub test again
---
 .../checkm2/predict/tests/main.nf.test        |  7 ++---
 .../checkm2/predict/tests/main.nf.test.snap   | 29 +++++++++++++++++++
 tests/config/nf-test.config                   |  3 +-
 3 files changed, 33 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test b/modules/nf-core/checkm2/predict/tests/main.nf.test
index de2a3c85910..1e64ff4dde3 100644
--- a/modules/nf-core/checkm2/predict/tests/main.nf.test
+++ b/modules/nf-core/checkm2/predict/tests/main.nf.test
@@ -9,9 +9,7 @@ nextflow_process {
     script "modules/nf-core/checkm2/predict/main.nf"
     process "CHECKM2_PREDICT"
 
-    test("Test CheckM2 Predict") {
-
-        setup {
+    setup {
             run("CHECKM2_DATABASEDOWNLOAD") {
                 script "../../databasedownload/main.nf"
                 process {
@@ -22,6 +20,8 @@ nextflow_process {
             }
         }
 
+    test("Test CheckM2 Predict") {
+
         when {
             params {
                 outdir = "${launchDir}/tests/results"
@@ -40,7 +40,6 @@ nextflow_process {
                 { assert snapshot(process.out.checkm2_tsv, process.out.versions).match() }
             )
         }
-
     }
 
 }
\ No newline at end of file
diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap
index 4364c12f41b..9702543c337 100644
--- a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap
+++ b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap
@@ -1,4 +1,33 @@
 {
+    "Test CheckM2 Predict - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "checkm2_output": [
+                    
+                ],
+                "checkm2_tsv": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-07T15:20:27.358984"
+    },
     "Test CheckM2 Predict": {
         "content": [
             [
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index daaf2ffe2ff..d8350fafaea 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -27,9 +27,8 @@ profiles {
     }
     docker_self_hosted {
         docker.enabled          = true
-        docker.userEmulation    = false
         docker.fixOwnership     = true
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = '--platform=linux/amd64'
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'

From cb8e4c926f1e8de22aa1f1375e188bd844c693f8 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 7 Jan 2025 17:30:42 +0100
Subject: [PATCH 3/4] Update GitHub Actions (#7239)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
---
 .github/actions/nf-test-action/action.yml | 2 +-
 .github/workflows/lint.yml                | 2 +-
 .github/workflows/pytest-workflow.yml     | 4 ++--
 .github/workflows/wave.yml                | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index a6f2532f926..a2539a6ba2f 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -17,7 +17,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+    - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
       with:
         distribution: "temurin"
         java-version: "17"
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index c617c10ccae..a743b62a57a 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -120,7 +120,7 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
         with:
           distribution: "temurin"
           java-version: "17"
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index 7c0d70c77c2..ec33e8be0dd 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -258,7 +258,7 @@ jobs:
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
 
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
         with:
           distribution: "temurin"
           java-version: "17"
@@ -308,7 +308,7 @@ jobs:
 
       - name: Upload logs on failure
         if: failure()
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
         with:
           name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
           path: |
diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index b56ed4795d6..f4557eec329 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -31,7 +31,7 @@ jobs:
 
       - name: Find conda differences
         id: conda-diff
-        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
+        uses: tj-actions/changed-files@d6e91a2266cdb9d62096cebf1e8546899c6aa18f # v45
         with:
           json: true
           escape_json: false
@@ -40,7 +40,7 @@ jobs:
 
       - name: Find Dockerfile differences
         id: docker-diff
-        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
+        uses: tj-actions/changed-files@d6e91a2266cdb9d62096cebf1e8546899c6aa18f # v45
         with:
           json: true
           escape_json: false

From 70538021b9b92958afa73c697d0d5decea7aa9ca Mon Sep 17 00:00:00 2001
From: MazzaLab <t.mazza@operapadrepio.it>
Date: Tue, 7 Jan 2025 19:54:45 +0100
Subject: [PATCH 4/4] Added BBMAP/REPAIR submodule (#7249)

* New submodule: BBMAP/REPAIR

* BBMAP/repair snapshot added

* removed cpu setting in nextflow.config

---------

Co-authored-by: irongraft <mazza.tommaso@gmail.com>
---
 modules/nf-core/bbmap/repair/environment.yml  |   7 +
 modules/nf-core/bbmap/repair/main.nf          |  57 +++++++
 modules/nf-core/bbmap/repair/meta.yml         |  67 ++++++++
 .../nf-core/bbmap/repair/tests/main.nf.test   | 115 +++++++++++++
 .../bbmap/repair/tests/main.nf.test.snap      | 156 ++++++++++++++++++
 .../bbmap/repair/tests/nextflow.config        |   5 +
 modules/nf-core/bbmap/repair/tests/tags.yml   |   2 +
 7 files changed, 409 insertions(+)
 create mode 100644 modules/nf-core/bbmap/repair/environment.yml
 create mode 100644 modules/nf-core/bbmap/repair/main.nf
 create mode 100644 modules/nf-core/bbmap/repair/meta.yml
 create mode 100644 modules/nf-core/bbmap/repair/tests/main.nf.test
 create mode 100644 modules/nf-core/bbmap/repair/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/bbmap/repair/tests/nextflow.config
 create mode 100644 modules/nf-core/bbmap/repair/tests/tags.yml

diff --git a/modules/nf-core/bbmap/repair/environment.yml b/modules/nf-core/bbmap/repair/environment.yml
new file mode 100644
index 00000000000..4e65bfe6a99
--- /dev/null
+++ b/modules/nf-core/bbmap/repair/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::bbmap=39.13"
diff --git a/modules/nf-core/bbmap/repair/main.nf b/modules/nf-core/bbmap/repair/main.nf
new file mode 100644
index 00000000000..9c12be2cf53
--- /dev/null
+++ b/modules/nf-core/bbmap/repair/main.nf
@@ -0,0 +1,57 @@
+process BBMAP_REPAIR {
+    tag "$meta.id"
+    label 'process_single'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bbmap:39.13--he5f24ec_1':
+        'biocontainers/bbmap:39.13--he5f24ec_1' }"
+
+    input:
+    tuple val(meta), path(reads)
+    val(interleave)
+
+    output:
+    tuple val(meta), path("*_repaired.fastq.gz")         , emit: repaired
+    tuple val(meta), path("${prefix}_singleton.fastq.gz"), emit: singleton
+    path  "versions.yml"                                 , emit: versions
+    path  "*.log"                                        , emit: log
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    in_reads  = ( interleave )  ? "in=${reads[0]}" : "in=${reads[0]} in2=${reads[1]}"
+    out_reads = ( interleave )  ? "out=${prefix}_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
+                                : "out=${prefix}_1_repaired.fastq.gz out2=${prefix}_2_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
+    """
+    maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
+    repair.sh \\
+        -Xmx\$maxmem \\
+        $in_reads \\
+        $out_reads \\
+        threads=${task.cpus}
+        ${args} \\
+        &> ${prefix}.repair.sh.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        repair.sh: \$(repair.sh --version |& sed '2!d ; s/BBMap version //')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}_1_repaired.fastq.gz
+    echo "" | gzip > ${prefix}_2_repaired.fastq.gz
+    echo "" | gzip > ${prefix}_singleton.fastq.gz
+    touch ${prefix}.repair.sh.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        repair.sh: \$(repair.sh --version |& sed '2!d ; s/BBMap version //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bbmap/repair/meta.yml b/modules/nf-core/bbmap/repair/meta.yml
new file mode 100644
index 00000000000..9190cd99c5e
--- /dev/null
+++ b/modules/nf-core/bbmap/repair/meta.yml
@@ -0,0 +1,67 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "bbmap_repair"
+description: Re-pairs reads that became disordered or had some mates eliminated.
+keywords:
+  - paired reads re-pairing
+  - fastq
+  - preprocessing
+tools:
+  - repair:
+      description: Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated
+        tools.
+      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
+      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/
+      licence: ["UC-LBL license (see package)"]
+      identifier: biotools:bbmap
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reads:
+        type: file
+        description: |
+          List of input paired end fastq files
+        pattern: "*.{fastq,fq}.gz"
+  - - interleave:
+        type: boolean
+        description: |
+          Indicates whether the input paired reads are interleaved or not
+output:
+  - repaired:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*_repaired.fastq.gz":
+          type: file
+          description: re-paired reads
+          pattern: "*_repaired.fastq.gz"
+  - singleton:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "${prefix}_singleton.fastq.gz":
+          type: file
+          description: singleton reads
+          pattern: "*singleton.fastq.gz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+  - log:
+      - "*.log":
+          type: file
+          description: log file containing stdout and stderr from repair.sh
+          pattern: "*.log"
+authors:
+  - "@mazzalab"
+maintainers:
+  - "@mazzalab"
+  - "@tm4zza"
diff --git a/modules/nf-core/bbmap/repair/tests/main.nf.test b/modules/nf-core/bbmap/repair/tests/main.nf.test
new file mode 100644
index 00000000000..ea6ff0f3664
--- /dev/null
+++ b/modules/nf-core/bbmap/repair/tests/main.nf.test
@@ -0,0 +1,115 @@
+nextflow_process {
+
+    name "Test Process BBMAP_REPAIR"
+    script "../main.nf"
+    process "BBMAP_REPAIR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bbmap"
+    tag "bbmap/repair"
+
+    test("sarscov2_illumina_paired - fastq_gz") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                module_args = 'qin=33'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                    ]
+                input[1] = false
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2_illumina_interleaved - fastq_gz") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                module_args = 'qin=33'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)]
+                    ]
+                input[1] = true
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2_illumina_paired - fastq_gz - stub") {
+        config "./nextflow.config"
+        options "-stub"
+
+        when {
+            params {
+                module_args = 'qin=33'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                    ]
+                input[1] = false
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2_illumina_interleaved - fastq_gz - stub") {
+        config "./nextflow.config"
+        options "-stub"
+
+        when {
+            params {
+                module_args = 'qin=33'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)]
+                    ]
+                input[1] = true
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/bbmap/repair/tests/main.nf.test.snap b/modules/nf-core/bbmap/repair/tests/main.nf.test.snap
new file mode 100644
index 00000000000..54e929b0611
--- /dev/null
+++ b/modules/nf-core/bbmap/repair/tests/main.nf.test.snap
@@ -0,0 +1,156 @@
+{
+    "sarscov2_illumina_paired - fastq_gz": {
+        "content": [
+            [
+                "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:01:18.284624712"
+    },
+    "sarscov2_illumina_interleaved - fastq_gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ],
+                "3": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "log": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "repaired": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "singleton": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:02:01.385727451"
+    },
+    "sarscov2_illumina_interleaved - fastq_gz": {
+        "content": [
+            [
+                "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:01:32.752620818"
+    },
+    "sarscov2_illumina_paired - fastq_gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ],
+                "3": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "log": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "repaired": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "singleton": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:01:47.341193946"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bbmap/repair/tests/nextflow.config b/modules/nf-core/bbmap/repair/tests/nextflow.config
new file mode 100644
index 00000000000..6b9f0bf755b
--- /dev/null
+++ b/modules/nf-core/bbmap/repair/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: BBMAP_REPAIR {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/bbmap/repair/tests/tags.yml b/modules/nf-core/bbmap/repair/tests/tags.yml
new file mode 100644
index 00000000000..a6e491df28f
--- /dev/null
+++ b/modules/nf-core/bbmap/repair/tests/tags.yml
@@ -0,0 +1,2 @@
+bbmap/repair:
+  - "modules/nf-core/bbmap/repair/**"