From bb3ec8984b4c5fb8180ac485cb45c16b7be98797 Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 07:53:15 +0000
Subject: [PATCH 01/12] Add output index type to samtools view

---
 modules/nf-core/samtools/view/main.nf         |  36 +-
 .../samtools/view/tests/cram_index.config     |   3 +
 .../nf-core/samtools/view/tests/main.nf.test  | 249 ++++++
 .../samtools/view/tests/main.nf.test.snap     | 724 ++++++++++++++----
 4 files changed, 867 insertions(+), 145 deletions(-)
 create mode 100644 modules/nf-core/samtools/view/tests/cram_index.config

diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index a6941e63888..3aa8f83c8ea 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -11,6 +11,7 @@ process SAMTOOLS_VIEW {
     tuple val(meta), path(input), path(index)
     tuple val(meta2), path(fasta)
     path qname
+    val index_format
 
     output:
     tuple val(meta), path("${prefix}.bam"),                                    emit: bam,              optional: true
@@ -20,7 +21,7 @@ process SAMTOOLS_VIEW {
     tuple val(meta), path("${prefix}.${file_type}.csi"),                       emit: csi,              optional: true
     tuple val(meta), path("${prefix}.${file_type}.crai"),                      emit: crai,             optional: true
     tuple val(meta), path("${prefix}.unselected.${file_type}"),                emit: unselected,       optional: true
-    tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true
+    tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"),     emit: unselected_index, optional: true
     path  "versions.yml",                                                      emit: versions
 
     when:
@@ -35,8 +36,19 @@ process SAMTOOLS_VIEW {
                 args.contains("--output-fmt bam") ? "bam" :
                 args.contains("--output-fmt cram") ? "cram" :
                 input.getExtension()
+
+    output_file = index_format ? "${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_format}" : "${prefix}.${file_type}"
+    // Can't choose index type of unselected file
     readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": ""
+
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if (index_format) {
+        if (!index_format.matches('bai|csi|crai')) {
+            error "Index format not one of bai, csi, crai."
+        } else if (file_type == "sam") {
+            error "Indexing not compatible with SAM output"
+        }
+    }
     """
     samtools \\
         view \\
@@ -44,7 +56,7 @@ process SAMTOOLS_VIEW {
         ${reference} \\
         ${readnames} \\
         $args \\
-        -o ${prefix}.${file_type} \\
+        -o ${output_file} \\
         $input \\
         $args2
 
@@ -61,13 +73,27 @@ process SAMTOOLS_VIEW {
                 args.contains("--output-fmt bam") ? "bam" :
                 args.contains("--output-fmt cram") ? "cram" :
                 input.getExtension()
-    if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-
-    index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""
+    default_index_format =
+        file_type == "bam" ? "csi" :
+        file_type == "cram" ? "crai" : ""
+    index = args.contains("--write-index") && index_format ? "touch ${prefix}.${file_type}.${index_format}" : args.contains("--write-index") ? "touch ${prefix}.${file_type}.${default_index_format}" : ""
+    unselected = qname ? "touch ${prefix}.unselected.${file_type}" : ""
+    // Can't choose index type of unselected file
+    unselected_index = qname && args.contains("--write-index") ? "touch ${prefix}.unselected.${file_type}.${default_index_format}" : ""
 
+    if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if (index_format) {
+        if (!index_format.matches('bai|csi|crai')) {
+            error "Index format not one of bai, csi, crai."
+        } else if (file_type == "sam") {
+            error "Indexing not compatible with SAM output."
+        }
+    }
     """
     touch ${prefix}.${file_type}
     ${index}
+    ${unselected}
+    ${unselected_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/view/tests/cram_index.config b/modules/nf-core/samtools/view/tests/cram_index.config
new file mode 100644
index 00000000000..ed87c3349db
--- /dev/null
+++ b/modules/nf-core/samtools/view/tests/cram_index.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "--output-fmt cram --write-index"
+}
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test
index 37b81a91630..d8551dd8c6b 100644
--- a/modules/nf-core/samtools/view/tests/main.nf.test
+++ b/modules/nf-core/samtools/view/tests/main.nf.test
@@ -21,6 +21,7 @@ nextflow_process {
                 ])
                 input[1] = [[],[]]
                 input[2] = []
+                input[3] = []
                 """
             }
         }
@@ -39,6 +40,135 @@ nextflow_process {
         }
     }
 
+    test("bam_csi_index") {
+
+        config "./bam_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = []
+                input[3] = 'csi'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions).match()
+                }
+            )
+        }
+    }
+
+    test("bam_bai_index") {
+
+        config "./bam_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = []
+                input[3] = 'bai'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.bai[0][1]).name,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("bam_bai_index_unselected") {
+
+        config "./bam_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = Channel.of('testN:1')
+                    .collectFile(name: 'selected_reads.txt')
+                input[3] = 'bai'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.bai[0][1]).name,
+                    file(process.out.unselected[0][1]).name,
+                    file(process.out.unselected_index[0][1]).name,
+                    process.out.versions).match()
+                }
+            )
+        }
+    }
+
+    test("cram_crai_index_unselected") {
+
+        config "./cram_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = Channel.of('testN:1')
+                    .collectFile(name: 'selected_reads.txt')
+                input[3] = 'crai'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.cram[0][1]).name,
+                    file(process.out.crai[0][1]).name,
+                    file(process.out.unselected[0][1]).name,
+                    file(process.out.unselected_index[0][1]).name,
+                    process.out.versions).match()
+                }
+            )
+        }
+    }
+
     test("cram") {
 
         when {
@@ -54,6 +184,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[2] = []
+                input[3] = []
                 """
             }
         }
@@ -89,6 +220,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[2] = []
+                input[3] = []
                 """
             }
         }
@@ -124,6 +256,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[2] = []
+                input[3] = []
                 """
             }
         }
@@ -159,6 +292,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true)
+                input[3] = []
                 """
             }
         }
@@ -194,6 +328,7 @@ nextflow_process {
                 ])
                 input[1] = [[],[]]
                 input[2] = []
+                input[3] = []
                 """
             }
         }
@@ -211,4 +346,118 @@ nextflow_process {
             )
         }
     }
+
+    test("bam_csi_index - stub") {
+
+        options "-stub"
+        config "./bam_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = []
+                input[3] = 'csi'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bam_bai_index - stub") {
+
+        options "-stub"
+        config "./bam_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = []
+                input[3] = 'bai'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bam_bai_index_uselected - stub") {
+
+        options "-stub"
+        config "./bam_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = Channel.of('testN:1')
+                    .collectFile(name: 'selected_reads.txt')
+                input[3] = 'bai'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("cram_crai_index_unselected - stub") {
+
+        options "-stub"
+        config "./cram_index.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    []
+                ])
+                input[1] = [[],[]]
+                input[2] = Channel.of('testN:1')
+                    .collectFile(name: 'selected_reads.txt')
+                input[3] = 'crai'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap
index 63849b037b7..1cb793f2700 100644
--- a/modules/nf-core/samtools/view/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap
@@ -9,16 +9,6 @@
         },
         "timestamp": "2024-02-12T19:37:51.256068"
     },
-    "cram_to_bam_index_csi": {
-        "content": [
-            "test.bam.csi"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:12.958617"
-    },
     "bam_stub_bam": {
         "content": [
             "test.bam"
@@ -60,36 +50,32 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-16T09:26:24.461775464"
+        "timestamp": "2025-02-14T07:43:43.6526401"
     },
-    "cram_to_bam_index_cram": {
+    "cram_to_bam_index_qname_csi": {
         "content": [
-            [
-                
-            ]
+            "test.bam.csi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:12.972288"
+        "timestamp": "2024-02-12T19:38:23.325496"
     },
-    "cram_to_bam_sam": {
+    "cram_to_bam_index_qname_unselected_csi": {
         "content": [
-            [
-                
-            ]
+            "test.unselected.bam.csi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:04.999247"
+        "timestamp": "2024-02-12T19:38:23.328458"
     },
-    "cram_to_bam_index_sam": {
+    "bam_csi": {
         "content": [
             [
                 
@@ -99,55 +85,182 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:12.976457"
+        "timestamp": "2024-02-12T19:37:51.262882"
     },
-    "cram_crai": {
+    "cram_to_bam_index_bam": {
         "content": [
-            [
-                
-            ]
+            "test.bam"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:56.497581"
+        "timestamp": "2024-02-12T19:38:12.95456"
     },
-    "cram_csi": {
+    "cram_to_bam_index_versions": {
         "content": [
             [
-                
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-12T19:37:56.50038"
+        "timestamp": "2024-09-16T09:25:14.475388399"
     },
-    "cram_to_bam_cram": {
+    "bam_csi_index": {
         "content": [
+            "test.bam",
+            "test.bam.csi",
             [
-                
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-02-12T19:38:04.992239"
+        "timestamp": "2025-02-14T07:45:19.718077276"
     },
-    "cram_to_bam_index_qname_csi": {
+    "bam_versions": {
         "content": [
-            "test.bam.csi"
+            [
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-13T16:13:00.739468586"
+    },
+    "cram_crai_index_unselected - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "unselected_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T07:47:20.903462221"
+    },
+    "bam_crai": {
+        "content": [
+            [
+                
+            ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:23.325496"
+        "timestamp": "2024-02-12T19:37:51.259774"
     },
-    "bam_stub_sam": {
+    "bam_cram": {
         "content": [
             [
                 
@@ -157,29 +270,33 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:32.079529"
+        "timestamp": "2024-02-12T19:37:51.261287"
     },
-    "cram_cram": {
+    "cram_sam": {
         "content": [
-            "test.cram"
+            [
+                
+            ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:56.490286"
+        "timestamp": "2024-02-12T19:37:56.502625"
     },
-    "cram_to_bam_index_qname_unselected_csi": {
+    "cram_versions": {
         "content": [
-            "test.unselected.bam.csi"
+            [
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-02-12T19:38:23.328458"
+        "timestamp": "2025-02-13T16:33:28.319991831"
     },
-    "bam_csi": {
+    "cram_to_bam_index_bai": {
         "content": [
             [
                 
@@ -189,9 +306,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:51.262882"
+        "timestamp": "2024-02-12T19:38:12.962863"
     },
-    "cram_to_bam_crai": {
+    "cram_to_bam_index_qname_sam": {
         "content": [
             [
                 
@@ -201,65 +318,247 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:04.989247"
+        "timestamp": "2024-02-12T19:38:23.337634"
     },
-    "cram_to_bam_index_crai": {
+    "bam_csi_index - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T07:46:52.477256747"
+    },
+    "cram_to_bam_index_csi": {
         "content": [
-            [
-                
-            ]
+            "test.bam.csi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:12.967681"
+        "timestamp": "2024-02-12T19:38:12.958617"
     },
-    "cram_to_bam_index_qname_versions": {
+    "bam_bai_index": {
         "content": [
+            "test.bam",
+            "test.bam.bai",
             [
                 "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-16T09:25:51.953436682"
+        "timestamp": "2025-02-14T07:45:29.205677197"
     },
-    "cram_to_bam_bam": {
+    "cram_to_bam_index_cram": {
         "content": [
-            "test.bam"
+            [
+                
+            ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:04.982361"
+        "timestamp": "2024-02-12T19:38:12.972288"
     },
-    "cram_to_bam_index_bam": {
+    "bam_bai_index - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T07:51:10.220507926"
+    },
+    "cram_to_bam_sam": {
         "content": [
-            "test.bam"
+            [
+                
+            ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:12.95456"
+        "timestamp": "2024-02-12T19:38:04.999247"
     },
-    "cram_to_bam_index_versions": {
+    "cram_to_bam_index_sam": {
         "content": [
             [
-                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
         },
-        "timestamp": "2024-09-16T09:25:14.475388399"
+        "timestamp": "2024-02-12T19:38:12.976457"
     },
-    "cram_to_bam_bai": {
+    "cram_crai": {
         "content": [
             [
                 
@@ -269,21 +568,21 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:04.98601"
+        "timestamp": "2024-02-12T19:37:56.497581"
     },
-    "cram_to_bam_versions": {
+    "cram_csi": {
         "content": [
             [
-                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
         },
-        "timestamp": "2024-09-16T09:24:49.673441798"
+        "timestamp": "2024-02-12T19:37:56.50038"
     },
-    "cram_bam": {
+    "cram_to_bam_cram": {
         "content": [
             [
                 
@@ -293,9 +592,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:56.495512"
+        "timestamp": "2024-02-12T19:38:04.992239"
     },
-    "bam_stub_cram": {
+    "bam_stub_sam": {
         "content": [
             [
                 
@@ -305,21 +604,19 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:32.076908"
+        "timestamp": "2024-02-12T19:38:32.079529"
     },
-    "cram_to_bam_index_qname_bai": {
+    "cram_cram": {
         "content": [
-            [
-                
-            ]
+            "test.cram"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:23.328458"
+        "timestamp": "2024-02-12T19:37:56.490286"
     },
-    "cram_to_bam_index_qname_crai": {
+    "cram_to_bam_crai": {
         "content": [
             [
                 
@@ -329,9 +626,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:23.330789"
+        "timestamp": "2024-02-12T19:38:04.989247"
     },
-    "cram_bai": {
+    "cram_to_bam_index_crai": {
         "content": [
             [
                 
@@ -341,63 +638,71 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:56.493129"
+        "timestamp": "2024-02-12T19:38:12.967681"
     },
-    "bam_stub_crai": {
+    "cram_crai_index_unselected": {
         "content": [
+            "test.cram",
+            "test.cram.crai",
+            "test.unselected.cram",
+            "test.unselected.cram.crai",
             [
-                
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-02-12T19:38:32.074313"
+        "timestamp": "2025-02-14T07:45:48.461930073"
     },
-    "cram_to_bam_index_qname_bam": {
+    "cram_to_bam_index_qname_versions": {
         "content": [
-            "test.bam"
+            [
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-12T19:38:23.322874"
+        "timestamp": "2024-09-16T09:25:51.953436682"
     },
-    "cram_to_bam_index_qname_unselected": {
+    "cram_to_bam_bam": {
         "content": [
-            "test.unselected.bam"
+            "test.bam"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:23.322874"
+        "timestamp": "2024-02-12T19:38:04.982361"
     },
-    "cram_to_bam_index_qname_unselected_csi": {
+    "cram_to_bam_bai": {
         "content": [
-            "test.unselected.bam.csi"
+            [
+                
+            ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:23.328458"
+        "timestamp": "2024-02-12T19:38:04.98601"
     },
-    "bam_versions": {
+    "cram_to_bam_versions": {
         "content": [
             [
                 "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-16T09:23:27.151650338"
+        "timestamp": "2025-02-13T16:33:39.363718229"
     },
-    "cram_to_bam_index_qname_cram": {
+    "cram_bam": {
         "content": [
             [
                 
@@ -407,9 +712,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:23.333248"
+        "timestamp": "2024-02-12T19:37:56.495512"
     },
-    "bam_crai": {
+    "bam_stub_cram": {
         "content": [
             [
                 
@@ -419,9 +724,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:51.259774"
+        "timestamp": "2024-02-12T19:38:32.076908"
     },
-    "bam_cram": {
+    "cram_to_bam_index_qname_bai": {
         "content": [
             [
                 
@@ -431,9 +736,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:51.261287"
+        "timestamp": "2024-02-12T19:38:23.328458"
     },
-    "cram_to_bam_csi": {
+    "cram_to_bam_index_qname_crai": {
         "content": [
             [
                 
@@ -443,9 +748,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:04.995454"
+        "timestamp": "2024-02-12T19:38:23.330789"
     },
-    "cram_sam": {
+    "cram_bai": {
         "content": [
             [
                 
@@ -455,23 +760,23 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:56.502625"
+        "timestamp": "2024-02-12T19:37:56.493129"
     },
-    "cram_versions": {
+    "bam_stub_crai": {
         "content": [
             [
-                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
         },
-        "timestamp": "2024-09-16T09:24:12.95416913"
+        "timestamp": "2024-02-12T19:38:32.074313"
     },
-    "cram_to_bam_index_qname_unselected": {
+    "cram_to_bam_index_qname_bam": {
         "content": [
-            "test.unselected.bam"
+            "test.bam"
         ],
         "meta": {
             "nf-test": "0.8.4",
@@ -479,7 +784,23 @@
         },
         "timestamp": "2024-02-12T19:38:23.322874"
     },
-    "bam_sam": {
+    "bam_bai_index_unselected": {
+        "content": [
+            "test.bam",
+            "test.bam.bai",
+            "test.unselected.bam",
+            "test.unselected.bam.csi",
+            [
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T07:45:38.993014707"
+    },
+    "cram_to_bam_index_qname_cram": {
         "content": [
             [
                 
@@ -489,9 +810,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:37:51.264651"
+        "timestamp": "2024-02-12T19:38:23.333248"
     },
-    "cram_to_bam_index_bai": {
+    "cram_to_bam_csi": {
         "content": [
             [
                 
@@ -501,9 +822,132 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:12.962863"
+        "timestamp": "2024-02-12T19:38:04.995454"
     },
-    "cram_to_bam_index_qname_sam": {
+    "bam_bai_index_uselected - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "unselected_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T07:51:24.947216832"
+    },
+    "cram_to_bam_index_qname_unselected": {
+        "content": [
+            "test.unselected.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.322874"
+    },
+    "bam_sam": {
         "content": [
             [
                 
@@ -513,7 +957,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-12T19:38:23.337634"
+        "timestamp": "2024-02-12T19:37:51.264651"
     },
     "bam_stub_csi": {
         "content": [

From ca0e2d98798f3dab538a57c21c0049da688ea58b Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 08:05:58 +0000
Subject: [PATCH 02/12] fix modules/subworkflows with samtools view

---
 modules/nf-core/yahs/tests/main.nf.test                   | 5 +++--
 subworkflows/nf-core/bam_split_by_region/main.nf          | 2 +-
 subworkflows/nf-core/bam_subsampledepth_samtools/main.nf  | 1 +
 .../nf-core/fastq_create_umi_consensus_fgbio/main.nf      | 2 +-
 tests/modules/nf-core/endorspy/main.nf                    | 8 ++++----
 tests/modules/nf-core/graphtyper/genotype/main.nf         | 6 +++---
 tests/modules/nf-core/leehom/main.nf                      | 2 +-
 tests/modules/nf-core/metaphlan3/metaphlan3/main.nf       | 2 +-
 8 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/yahs/tests/main.nf.test b/modules/nf-core/yahs/tests/main.nf.test
index ee53a110d92..27572cb21f4 100644
--- a/modules/nf-core/yahs/tests/main.nf.test
+++ b/modules/nf-core/yahs/tests/main.nf.test
@@ -26,13 +26,14 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[2] = []
+                input[3] = []
                 """
             }
             }
         }
 
     test("homo_sapiens-bam-fasta-fai") {
-        
+
         when {
             process {
                 """
@@ -50,5 +51,5 @@ nextflow_process {
             )
         }
     }
-    
+
 }
diff --git a/subworkflows/nf-core/bam_split_by_region/main.nf b/subworkflows/nf-core/bam_split_by_region/main.nf
index 82b00f3ce4c..71b4d01c4e3 100644
--- a/subworkflows/nf-core/bam_split_by_region/main.nf
+++ b/subworkflows/nf-core/bam_split_by_region/main.nf
@@ -45,7 +45,7 @@ workflow BAM_SPLIT_BY_REGION {
         .map{ meta, bam, bai, regions, chrom -> [ meta + [ genomic_region:chrom ], bam, bai ] }
 
     // The specified region is put into ext.args2 from the meta. See nextflow.config of the subworkflow.
-    SAMTOOLS_VIEW(ch_bam_for_splitting, [[],[]], [])
+    SAMTOOLS_VIEW(ch_bam_for_splitting, [[],[]], [], [])
     ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())
 
     //
diff --git a/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf b/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf
index b7f54e63046..754ff312c99 100644
--- a/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf
+++ b/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf
@@ -37,6 +37,7 @@ workflow BAM_SUBSAMPLEDEPTH_SAMTOOLS {
     SAMTOOLS_VIEW(
         ch_input_subsample,
         ch_fasta,
+        [],
         []
     )
     ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())
diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
index 661d79327d9..1138f3f3bd6 100644
--- a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
+++ b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
@@ -123,7 +123,7 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO {
         dummy_bam_bai = ZIPPERBAMS_PRE.out.bam.map{meta, bam -> [meta, bam, dummyIndexFile]}
         check_dummy_bam_bai = dummy_bam_bai.dump(tag: 'dummy_index')
         // then applying samtools view to filter only paired reads
-        BAMFILTER ( dummy_bam_bai, [[],[]], [] )
+        BAMFILTER ( dummy_bam_bai, [[],[]], [], [] )
         ch_versions = ch_versions.mix(BAMFILTER.out.versions)
         groupready_bam = BAMFILTER.out.bam
         // deleting dummy file
diff --git a/tests/modules/nf-core/endorspy/main.nf b/tests/modules/nf-core/endorspy/main.nf
index 0e747fedd7a..a324b1c87e1 100644
--- a/tests/modules/nf-core/endorspy/main.nf
+++ b/tests/modules/nf-core/endorspy/main.nf
@@ -35,7 +35,7 @@ workflow test_endorspy_raw_qualityfilter {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [] )
+    SAMTOOLS_VIEW ( input, [], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)
@@ -62,7 +62,7 @@ workflow test_endorspy_raw_qualityfilter_dedup {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [] )
+    SAMTOOLS_VIEW ( input, [], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)
@@ -91,7 +91,7 @@ workflow test_endorspy_raw_dedup {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [] )
+    SAMTOOLS_VIEW ( input, [], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)
@@ -117,7 +117,7 @@ workflow test_endorspy_qualityfilter_dedup {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [] )
+    SAMTOOLS_VIEW ( input, [], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)
diff --git a/tests/modules/nf-core/graphtyper/genotype/main.nf b/tests/modules/nf-core/graphtyper/genotype/main.nf
index bbeb4a1b166..006ec405b81 100644
--- a/tests/modules/nf-core/graphtyper/genotype/main.nf
+++ b/tests/modules/nf-core/graphtyper/genotype/main.nf
@@ -8,7 +8,7 @@ include { SAMTOOLS_VIEW                                     } from '../../../../
 include { SAMTOOLS_INDEX                                    } from '../../../../../modules/nf-core/samtools/index/main.nf'
 
 workflow test_graphtyper_genotype_single {
-    
+
     input = [
         [ id:'test' ], // meta map
         [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
@@ -22,7 +22,7 @@ workflow test_graphtyper_genotype_single {
 }
 
 workflow test_graphtyper_genotype_multi {
-    
+
     input = Channel.fromList ( [
         [
             [ id: 'test1' ], // meta map
@@ -40,7 +40,7 @@ workflow test_graphtyper_genotype_multi {
     ref_index = [ [ id: 'ref_index' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)]
     region = file(params.test_data['sarscov2']['genome']['regions_txt'], checkIfExists: true)
 
-    SAMTOOLS_VIEW ( input, reference, [])
+    SAMTOOLS_VIEW ( input, reference, [], [])
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.cram )
     cram_grouped = SAMTOOLS_VIEW.out.cram.map{ [[id: 'group'], it[1]] }.groupTuple()
     crai_grouped = SAMTOOLS_INDEX.out.crai.map{ [[id: 'group'], it[1]] }.groupTuple()
diff --git a/tests/modules/nf-core/leehom/main.nf b/tests/modules/nf-core/leehom/main.nf
index aeacd31bb75..de8e32d539a 100644
--- a/tests/modules/nf-core/leehom/main.nf
+++ b/tests/modules/nf-core/leehom/main.nf
@@ -12,7 +12,7 @@ workflow test_leehom_bam {
             []
         ]
 
-    SAMTOOLS_VIEW ( input, [] , [])
+    SAMTOOLS_VIEW ( input, [] , [], [])
     LEEHOM ( SAMTOOLS_VIEW.out.bam )
 }
 
diff --git a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
index 4a0f7948f5c..a1bb8607f2a 100644
--- a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
+++ b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
@@ -49,7 +49,7 @@ workflow test_metaphlan3_sam {
     db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    SAMTOOLS_VIEW ( input, [] )
+    SAMTOOLS_VIEW ( input, [], [] )
     METAPHLAN3_METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
 }
 

From aa151d88204f789e5896371dc1efb83249206daa Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 08:09:35 +0000
Subject: [PATCH 03/12] fix meta.yml

---
 modules/nf-core/samtools/view/meta.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml
index caa7b0150d4..53445916cc1 100644
--- a/modules/nf-core/samtools/view/meta.yml
+++ b/modules/nf-core/samtools/view/meta.yml
@@ -43,6 +43,10 @@ input:
         type: file
         description: Optional file with read names to output only select alignments
         pattern: "*.{txt,list}"
+  - - index_format:
+        type: string
+        description: Index format, used together with ext.args = '--write-index'
+        pattern: "*.{bai,csi,crai}"
 output:
   - bam:
       - meta:
@@ -120,10 +124,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.unselected.${file_type}.{bai,csi,crsi}:
+      - ${prefix}.unselected.${file_type}.{csi,crai}:
           type: file
           description: index for the "unselected" file
-          pattern: "*.unselected.{bai,csi,crai}"
+          pattern: "*.unselected.{csi,crai}"
   - versions:
       - versions.yml:
           type: file

From 09ce07601adb4bd8d60c874301bc8661be3576c8 Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 08:14:29 +0000
Subject: [PATCH 04/12] fix endorspy

---
 tests/modules/nf-core/endorspy/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/modules/nf-core/endorspy/main.nf b/tests/modules/nf-core/endorspy/main.nf
index a324b1c87e1..685fcca660d 100644
--- a/tests/modules/nf-core/endorspy/main.nf
+++ b/tests/modules/nf-core/endorspy/main.nf
@@ -35,7 +35,7 @@ workflow test_endorspy_raw_qualityfilter {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [], [] )
+    SAMTOOLS_VIEW ( input, [[],[]], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)
@@ -62,7 +62,7 @@ workflow test_endorspy_raw_qualityfilter_dedup {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [], [] )
+    SAMTOOLS_VIEW ( input, [[],[]], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)
@@ -91,7 +91,7 @@ workflow test_endorspy_raw_dedup {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [], [] )
+    SAMTOOLS_VIEW ( input, [[],[]], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)
@@ -117,7 +117,7 @@ workflow test_endorspy_qualityfilter_dedup {
 
 
     SAMTOOLS_FLAGSTAT1 ( input )
-    SAMTOOLS_VIEW ( input, [], [], [] )
+    SAMTOOLS_VIEW ( input, [[],[]], [], [] )
     SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
     input2 = SAMTOOLS_VIEW.out.bam
        .mix(SAMTOOLS_INDEX.out.bai)

From e7a0e94e5a1a125d7513af45c7d6def4bfbd610b Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 08:15:26 +0000
Subject: [PATCH 05/12] fix leehom

---
 tests/modules/nf-core/leehom/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/nf-core/leehom/main.nf b/tests/modules/nf-core/leehom/main.nf
index de8e32d539a..f76970572bc 100644
--- a/tests/modules/nf-core/leehom/main.nf
+++ b/tests/modules/nf-core/leehom/main.nf
@@ -12,7 +12,7 @@ workflow test_leehom_bam {
             []
         ]
 
-    SAMTOOLS_VIEW ( input, [] , [], [])
+    SAMTOOLS_VIEW ( input, [[],[]], [], [])
     LEEHOM ( SAMTOOLS_VIEW.out.bam )
 }
 

From 2c988a4950ad5da29901e7d710dbcf2ad0baac15 Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 08:16:48 +0000
Subject: [PATCH 06/12] fix graphtyper

---
 tests/modules/nf-core/graphtyper/genotype/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/nf-core/graphtyper/genotype/main.nf b/tests/modules/nf-core/graphtyper/genotype/main.nf
index 006ec405b81..90270f66b8b 100644
--- a/tests/modules/nf-core/graphtyper/genotype/main.nf
+++ b/tests/modules/nf-core/graphtyper/genotype/main.nf
@@ -35,7 +35,7 @@ workflow test_graphtyper_genotype_multi {
             file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
         ]
     ] )
-    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true).map { it -> [ [ 'id': it.simpleName], it ] }
     ref_with_meta = [ [ id: 'ref' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
     ref_index = [ [ id: 'ref_index' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)]
     region = file(params.test_data['sarscov2']['genome']['regions_txt'], checkIfExists: true)

From 0e3a3eca4ac82cdd7541109525d625a1852797ed Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 08:19:17 +0000
Subject: [PATCH 07/12] fix metaphlan3

---
 tests/modules/nf-core/metaphlan3/metaphlan3/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
index a1bb8607f2a..02b7c0a9b12 100644
--- a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
+++ b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
@@ -49,7 +49,7 @@ workflow test_metaphlan3_sam {
     db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    SAMTOOLS_VIEW ( input, [], [] )
+    SAMTOOLS_VIEW ( input, [[],[]], [], [] )
     METAPHLAN3_METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
 }
 

From 68b686d48181ae508c9f983faf23beadbc875fec Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 08:27:45 +0000
Subject: [PATCH 08/12] fix

---
 .../nf-core/fastq_create_umi_consensus_fgbio/main.nf         | 2 +-
 tests/modules/nf-core/graphtyper/genotype/main.nf            | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
index 1138f3f3bd6..175a2bda9e6 100644
--- a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
+++ b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
@@ -79,7 +79,7 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO {
         // appropriately tagged interleaved FASTQ reads are mapped to the reference
         // the aligner should be set with the following parameters "-p -K 150000000 -Y"
         // to be configured in ext.args of your config
-        BWAMEM1_MEM_PRE ( BAM2FASTQ_PRE.out.fastq, bwaindex, false )
+        BWAMEM1_MEM_PRE ( BAM2FASTQ_PRE.out.fastq, bwaindex, [[],[]], false )
         ch_versions = ch_versions.mix(BWAMEM1_MEM_PRE.out.versions)
         aligned_bam = aligned_bam.mix(BWAMEM1_MEM_PRE.out.bam)
     } else {
diff --git a/tests/modules/nf-core/graphtyper/genotype/main.nf b/tests/modules/nf-core/graphtyper/genotype/main.nf
index 90270f66b8b..d93f8c06f41 100644
--- a/tests/modules/nf-core/graphtyper/genotype/main.nf
+++ b/tests/modules/nf-core/graphtyper/genotype/main.nf
@@ -35,7 +35,10 @@ workflow test_graphtyper_genotype_multi {
             file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
         ]
     ] )
-    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true).map { it -> [ [ 'id': it.simpleName], it ] }
+    reference = Channel.of([
+        [ id: 'test_genome'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ])
     ref_with_meta = [ [ id: 'ref' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
     ref_index = [ [ id: 'ref_index' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)]
     region = file(params.test_data['sarscov2']['genome']['regions_txt'], checkIfExists: true)

From c148d2078af49413dfaedaa7142a4e8e5c2886bc Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 09:00:17 +0000
Subject: [PATCH 09/12] port bam split by region to nf-test

---
 .../bam_split_by_region/nextflow.config       |  14 ---
 .../bam_split_by_region/tests/main.nf.test    |  45 ++++++++
 .../tests/main.nf.test.snap                   | 102 ++++++++++++++++++
 .../bam_split_by_region/tests/nextflow.config |   6 ++
 tests/config/pytest_modules.yml               |   3 -
 .../nf-core/bam_split_by_region/main.nf       |  30 ------
 .../bam_split_by_region/nextflow.config       |  15 ---
 .../nf-core/bam_split_by_region/test.yml      |  35 ------
 8 files changed, 153 insertions(+), 97 deletions(-)
 delete mode 100644 subworkflows/nf-core/bam_split_by_region/nextflow.config
 create mode 100644 subworkflows/nf-core/bam_split_by_region/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap
 create mode 100644 subworkflows/nf-core/bam_split_by_region/tests/nextflow.config
 delete mode 100644 tests/subworkflows/nf-core/bam_split_by_region/main.nf
 delete mode 100644 tests/subworkflows/nf-core/bam_split_by_region/nextflow.config
 delete mode 100644 tests/subworkflows/nf-core/bam_split_by_region/test.yml

diff --git a/subworkflows/nf-core/bam_split_by_region/nextflow.config b/subworkflows/nf-core/bam_split_by_region/nextflow.config
deleted file mode 100644
index 92d3956fc3d..00000000000
--- a/subworkflows/nf-core/bam_split_by_region/nextflow.config
+++ /dev/null
@@ -1,14 +0,0 @@
-// IMPORTANT: Add this configuration to your modules.config
-
-process {
-    withName: ".*BAM_SPLIT_BY_REGION:SAMTOOLS_VIEW" {
-        ext.args2 = {
-            [
-                "${meta.genomic_region}", // Specifies the chromosome name used for splitting the input bam file.
-            ].join(' ').trim()
-        }
-
-        ext.prefix = { "${meta.id}_${meta.genomic_region}" }
-    }
-
-}
diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test
new file mode 100644
index 00000000000..6272399c4fc
--- /dev/null
+++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test
@@ -0,0 +1,45 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core subworkflows test bam_split_by_region
+nextflow_workflow {
+
+    name "Test Subworkflow BAM_SPLIT_BY_REGION"
+    script "../main.nf"
+    workflow "BAM_SPLIT_BY_REGION"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/bam_split_by_region"
+    tag "samtools"
+    tag "samtools/sort"
+    tag "samtools/index"
+
+    config "./nextflow.config"
+
+    test("homo_sapiens - test_paired_end_markduplicates_sorted_bam") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id: 'test', single_end: false ],
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.bam_bai.findAll { file(it.get(1)).name }.toSorted(),
+                    workflow.out.bam_bai.findAll { bam(it.get(1)).getReadsMD5() }.toSorted(),
+                    workflow.out.bam_bai.findAll { file(it.get(2)).name }.toSorted(),
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap
new file mode 100644
index 00000000000..a2a2e6c7bc0
--- /dev/null
+++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap
@@ -0,0 +1,102 @@
+{
+    "homo_sapiens - test_paired_end_markduplicates_sorted_bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:24132499-24910998"
+                    },
+                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
+                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:25689497-46709983"
+                    },
+                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
+                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:1-23354000"
+                    },
+                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
+                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:24132499-24910998"
+                    },
+                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
+                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:25689497-46709983"
+                    },
+                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
+                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:1-23354000"
+                    },
+                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
+                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:24132499-24910998"
+                    },
+                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
+                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:25689497-46709983"
+                    },
+                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
+                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
+                ],
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "genomic_region": "chr21:1-23354000"
+                    },
+                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
+                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
+                ]
+            ],
+            [
+                "versions.yml:md5,022ce36c7637b4c28f9e7a3b6d788543",
+                "versions.yml:md5,1430b8967dea6b0eb5a65313c8d81e81"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T08:59:50.32521715"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_split_by_region/tests/nextflow.config b/subworkflows/nf-core/bam_split_by_region/tests/nextflow.config
new file mode 100644
index 00000000000..7f5a8e20fe9
--- /dev/null
+++ b/subworkflows/nf-core/bam_split_by_region/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: "BAM_SPLIT_BY_REGION:SAMTOOLS_VIEW" {
+        ext.args2 = { "${meta.genomic_region}" } // Specifies the chromosome name used for splitting the input bam file.
+        ext.prefix = { "${meta.id}_${meta.genomic_region}" }
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index a0a212f4bb7..304d3ae8b74 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -426,9 +426,6 @@ subworkflows/bam_markduplicates_samtools:
 subworkflows/bam_ngscheckmate:
   - subworkflows/nf-core/bam_ngscheckmate/**
   - tests/subworkflows/nf-core/bam_ngscheckmate/**
-subworkflows/bam_split_by_region:
-  - subworkflows/nf-core/bam_split_by_region/**
-  - tests/subworkflows/nf-core/bam_split_by_region/**
 subworkflows/bam_tumor_normal_somatic_variant_calling_gatk:
   - subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**
   - tests/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**
diff --git a/tests/subworkflows/nf-core/bam_split_by_region/main.nf b/tests/subworkflows/nf-core/bam_split_by_region/main.nf
deleted file mode 100644
index eca873ba5bc..00000000000
--- a/tests/subworkflows/nf-core/bam_split_by_region/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_INDEX } from '../../../../modules/nf-core/samtools/index/main.nf'
-include { BAM_SPLIT_BY_REGION } from '../../../../subworkflows/nf-core/bam_split_by_region/main.nf'
-
-workflow test_bam_split_by_region {
-
-    input = [
-        [ [ id: 'test', single_end: false ],
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'],     checkIfExists: true),
-        ],
-        [ [ id: 'test2', single_end: false ],
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'],     checkIfExists: true),
-        ]
-    ]
-
-    regions = [
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'],     checkIfExists: true)
-    ]
-
-    SAMTOOLS_INDEX(Channel.fromList(input))
-
-    ch_bam_split_input=Channel.fromList(input)
-            .join(SAMTOOLS_INDEX.out.bai)
-            .combine(Channel.of(regions))
-
-    BAM_SPLIT_BY_REGION ( ch_bam_split_input )
-}
diff --git a/tests/subworkflows/nf-core/bam_split_by_region/nextflow.config b/tests/subworkflows/nf-core/bam_split_by_region/nextflow.config
deleted file mode 100644
index 308a615193c..00000000000
--- a/tests/subworkflows/nf-core/bam_split_by_region/nextflow.config
+++ /dev/null
@@ -1,15 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: ".*BAM_SPLIT_BY_REGION:SAMTOOLS_VIEW" {
-        ext.args2 = {
-            [
-                "${meta.genomic_region}", // Specifies the chromosome name used for splitting the input bam file.
-            ].join(' ').trim()
-        }
-
-        ext.prefix = { "${meta.id}_${meta.genomic_region}" }
-    }
-
-}
diff --git a/tests/subworkflows/nf-core/bam_split_by_region/test.yml b/tests/subworkflows/nf-core/bam_split_by_region/test.yml
deleted file mode 100644
index d0498742218..00000000000
--- a/tests/subworkflows/nf-core/bam_split_by_region/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: bam_split_by_region test_bam_split_by_region
-  command: nextflow run ./tests/subworkflows/nf-core/bam_split_by_region -entry test_bam_split_by_region -c ./tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools/index
-    - samtools/view
-    - subworkflows
-    - subworkflows/bam_split_by_region
-  files:
-    - path: output/samtools/test.paired_end.markduplicates.sorted.bam.bai
-      md5sum: 15f1723181368484a9c783323b6699e5
-    - path: output/samtools/test2_chr21:1-23354000.bam
-      md5sum: 1286f2e37ead72c89a6d46dd3550b5cf
-    - path: output/samtools/test2_chr21:1-23354000.bam.bai
-      md5sum: b344287b0d56c56dacd819a388783af4
-    - path: output/samtools/test2_chr21:24132499-24910998.bam
-      md5sum: d3f8e65b43b15f19813177206d5151df
-    - path: output/samtools/test2_chr21:24132499-24910998.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/samtools/test2_chr21:25689497-46709983.bam
-      md5sum: 3faa0c1d5219b9638af66bb89d27af6a
-    - path: output/samtools/test2_chr21:25689497-46709983.bam.bai
-      md5sum: d0dfe65baf9ebc857c95fe4bad1f5f9f
-    - path: output/samtools/test_chr21:1-23354000.bam
-      md5sum: c2392dc8e421b5a5bb6344a8aee3df01
-    - path: output/samtools/test_chr21:1-23354000.bam.bai
-      md5sum: adbf2a0b95a947c055c219f0d950add0
-    - path: output/samtools/test_chr21:24132499-24910998.bam
-      md5sum: 7e4f52bdc87c726369a962beb8153a4e
-    - path: output/samtools/test_chr21:24132499-24910998.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/samtools/test_chr21:25689497-46709983.bam
-      md5sum: c46656090a5a322ad68cc6b43cd6c84f
-    - path: output/samtools/test_chr21:25689497-46709983.bam.bai
-      md5sum: 50c7f05de7e4ea77d8400d5890466480

From 161a736e0da5b2e3e5bb50ab3b2621d72fe3892b Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 09:02:58 +0000
Subject: [PATCH 10/12] fix

---
 modules/nf-core/samtools/view/main.nf         |   6 +-
 .../nf-core/bam_split_by_region/README.md     |  14 ++
 .../bam_split_by_region/tests/main.nf.test    |  31 +++-
 .../tests/main.nf.test.snap                   | 169 +++++++++---------
 .../fastq_create_umi_consensus_fgbio/main.nf  |   2 +-
 5 files changed, 133 insertions(+), 89 deletions(-)
 create mode 100644 subworkflows/nf-core/bam_split_by_region/README.md

diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index cb13452cb91..f43a4c6e72b 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -37,7 +37,7 @@ process SAMTOOLS_VIEW {
                 args.contains("--output-fmt cram") ? "cram" :
                 input.getExtension()
 
-    output_file = index_format ? "${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_format}" : "${prefix}.${file_type}"
+    output_file = index_format ? "${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_format} --write-index" : "${prefix}.${file_type}"
     // Can't choose index type of unselected file
     readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": ""
 
@@ -76,10 +76,10 @@ process SAMTOOLS_VIEW {
     default_index_format =
         file_type == "bam" ? "csi" :
         file_type == "cram" ? "crai" : ""
-    index = args.contains("--write-index") && index_format ? "touch ${prefix}.${file_type}.${index_format}" : args.contains("--write-index") ? "touch ${prefix}.${file_type}.${default_index_format}" : ""
+    index =  index_format ? "touch ${prefix}.${file_type}.${index_format}" : args.contains("--write-index") ? "touch ${prefix}.${file_type}.${default_index_format}" : ""
     unselected = qname ? "touch ${prefix}.unselected.${file_type}" : ""
     // Can't choose index type of unselected file
-    unselected_index = qname && args.contains("--write-index") ? "touch ${prefix}.unselected.${file_type}.${default_index_format}" : ""
+    unselected_index = qname && (args.contains("--write-index") || index_format) ? "touch ${prefix}.unselected.${file_type}.${default_index_format}" : ""
 
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     if (index_format) {
diff --git a/subworkflows/nf-core/bam_split_by_region/README.md b/subworkflows/nf-core/bam_split_by_region/README.md
new file mode 100644
index 00000000000..92d3956fc3d
--- /dev/null
+++ b/subworkflows/nf-core/bam_split_by_region/README.md
@@ -0,0 +1,14 @@
+// IMPORTANT: Add this configuration to your modules.config
+
+process {
+    withName: ".*BAM_SPLIT_BY_REGION:SAMTOOLS_VIEW" {
+        ext.args2 = {
+            [
+                "${meta.genomic_region}", // Specifies the chromosome name used for splitting the input bam file.
+            ].join(' ').trim()
+        }
+
+        ext.prefix = { "${meta.id}_${meta.genomic_region}" }
+    }
+
+}
diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test
index 6272399c4fc..1cee46a8947 100644
--- a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test
+++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test
@@ -34,12 +34,37 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.bam_bai.findAll { file(it.get(1)).name }.toSorted(),
-                    workflow.out.bam_bai.findAll { bam(it.get(1)).getReadsMD5() }.toSorted(),
-                    workflow.out.bam_bai.findAll { file(it.get(2)).name }.toSorted(),
+                    workflow.out.bam_bai.toSorted { a, b -> file(a.get(1)).name <=> file(b.get(1)).name }.collect { file(it.get(1)).name },
+                    workflow.out.bam_bai.toSorted { a, b -> file(a.get(1)).name <=> file(b.get(1)).name }.collect { bam(it.get(1)).getReadsMD5() },
+                    workflow.out.bam_bai.toSorted { a, b -> file(a.get(1)).name <=> file(b.get(1)).name }.collect { file(it.get(2)).name },
                     workflow.out.versions
                 ).match() }
             )
         }
     }
+
+    test("homo_sapiens - test_paired_end_markduplicates_sorted_bam - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id: 'test', single_end: false ],
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path +'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
 }
diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap
index a2a2e6c7bc0..5b8566fa0f8 100644
--- a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap
@@ -2,91 +2,19 @@
     "homo_sapiens - test_paired_end_markduplicates_sorted_bam": {
         "content": [
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:24132499-24910998"
-                    },
-                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
-                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
-                ],
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:25689497-46709983"
-                    },
-                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
-                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
-                ],
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:1-23354000"
-                    },
-                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
-                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
-                ]
+                "test_chr21:1-23354000.bam",
+                "test_chr21:24132499-24910998.bam",
+                "test_chr21:25689497-46709983.bam"
             ],
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:24132499-24910998"
-                    },
-                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
-                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
-                ],
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:25689497-46709983"
-                    },
-                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
-                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
-                ],
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:1-23354000"
-                    },
-                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
-                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
-                ]
+                "a2288aed3c12eb43e20164dc85787fad",
+                "d41d8cd98f00b204e9800998ecf8427e",
+                "831a9c955bc0fbfe24da0b16ffee4365"
             ],
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:24132499-24910998"
-                    },
-                    "test_chr21:24132499-24910998.bam:md5,649908006f4333ef13e42313e0885d96",
-                    "test_chr21:24132499-24910998.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
-                ],
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:25689497-46709983"
-                    },
-                    "test_chr21:25689497-46709983.bam:md5,c4bc65ad94bde9cc901d33e964a977c6",
-                    "test_chr21:25689497-46709983.bam.bai:md5,834238b87a13404627fecaa1ed7ae4f4"
-                ],
-                [
-                    {
-                        "id": "test",
-                        "single_end": false,
-                        "genomic_region": "chr21:1-23354000"
-                    },
-                    "test_chr21:1-23354000.bam:md5,e17b22b80b4ba098232f12a3cb612c73",
-                    "test_chr21:1-23354000.bam.bai:md5,adbf2a0b95a947c055c219f0d950add0"
-                ]
+                "test_chr21:1-23354000.bam.bai",
+                "test_chr21:24132499-24910998.bam.bai",
+                "test_chr21:25689497-46709983.bam.bai"
             ],
             [
                 "versions.yml:md5,022ce36c7637b4c28f9e7a3b6d788543",
@@ -97,6 +25,83 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-14T08:59:50.32521715"
+        "timestamp": "2025-02-14T09:29:31.729957588"
+    },
+    "homo_sapiens - test_paired_end_markduplicates_sorted_bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "genomic_region": "chr21:1-23354000"
+                        },
+                        "test_chr21:1-23354000.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_chr21:1-23354000.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "genomic_region": "chr21:24132499-24910998"
+                        },
+                        "test_chr21:24132499-24910998.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_chr21:24132499-24910998.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "genomic_region": "chr21:25689497-46709983"
+                        },
+                        "test_chr21:25689497-46709983.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_chr21:25689497-46709983.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,022ce36c7637b4c28f9e7a3b6d788543",
+                    "versions.yml:md5,1430b8967dea6b0eb5a65313c8d81e81"
+                ],
+                "bam_bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "genomic_region": "chr21:1-23354000"
+                        },
+                        "test_chr21:1-23354000.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_chr21:1-23354000.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "genomic_region": "chr21:24132499-24910998"
+                        },
+                        "test_chr21:24132499-24910998.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_chr21:24132499-24910998.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "genomic_region": "chr21:25689497-46709983"
+                        },
+                        "test_chr21:25689497-46709983.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_chr21:25689497-46709983.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,022ce36c7637b4c28f9e7a3b6d788543",
+                    "versions.yml:md5,1430b8967dea6b0eb5a65313c8d81e81"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-14T09:01:38.813440955"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
index 175a2bda9e6..ab88ca1763a 100644
--- a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
+++ b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf
@@ -157,7 +157,7 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO {
         // using the above created groups, a consensus across reads in the same group
         // can be called
         // this will emit a consensus BAM file
-        CALLUMICONSENSUS ( GROUPREADSBYUMI.out.bam )
+        CALLUMICONSENSUS ( GROUPREADSBYUMI.out.bam, [], [])
         ch_versions = ch_versions.mix(CALLUMICONSENSUS.out.versions)
         consensus_bam =  CALLUMICONSENSUS.out.bam
     }

From 16f4dc272a9f6d85c5f9afebc4e6a0e361c192ce Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Fri, 14 Feb 2025 10:31:30 +0000
Subject: [PATCH 11/12] try to fix CI

---
 .github/workflows/lint.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index fdc7c8f799b..2ff67a4fa39 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -85,10 +85,11 @@ jobs:
           script: |
             return [...new Set(${{ steps.filter.outputs.modules_files }}
               .map(path => path
+                .replace('tests/modules/nf-core/', '')
                 .replace('modules/nf-core/', '')
                 .split('/')
                 .slice(0, 2)
-                .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.md'))
+                .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && x !== 'nextflow.config' && x !== 'test.yml' && !x.endsWith('.md'))
                 .join('/'))
               )
             ];

From 0b87a4889e58b0fb4b2f85503fc7d13dadea9fb1 Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Wed, 19 Feb 2025 08:38:53 +0000
Subject: [PATCH 12/12] Don't check tests folder at all

---
 .github/workflows/lint.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 2ff67a4fa39..d7e110d03bf 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -71,10 +71,8 @@ jobs:
           filters: |
             modules:
               - added|modified: 'modules/nf-core/**'
-              - added|modified: 'tests/modules/nf-core/**'
             subworkflows:
               - added|modified: 'subworkflows/nf-core/**'
-              - added|modified: 'tests/subworkflows/nf-core/**'
           token: ""
           list-files: "json"
 
@@ -85,11 +83,10 @@ jobs:
           script: |
             return [...new Set(${{ steps.filter.outputs.modules_files }}
               .map(path => path
-                .replace('tests/modules/nf-core/', '')
                 .replace('modules/nf-core/', '')
                 .split('/')
                 .slice(0, 2)
-                .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && x !== 'nextflow.config' && x !== 'test.yml' && !x.endsWith('.md'))
+                .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.md'))
                 .join('/'))
               )
             ];