diff --git a/CHANGELOG.md b/CHANGELOG.md
index 55d93338b1..f2a41871f6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [1669](https://github.com/nf-core/sarek/pull/1669) - Better nf-test pipeline level tests
+- [1675](https://github.com/nf-core/sarek/pull/1675) - Migrate pytest aligner tests to nf-test
 
 ### Fixed
 
diff --git a/tests/aligner-bwa-mem.nf.test b/tests/aligner-bwa-mem.nf.test
new file mode 100644
index 0000000000..69da12cd97
--- /dev/null
+++ b/tests/aligner-bwa-mem.nf.test
@@ -0,0 +1,74 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --aligner bwa-mem --save_reference | skip QC/recal/md") {
+
+        when {
+            params {
+                aligner = 'bwa-mem'
+                outdir = "$outputDir"
+                save_reference = true
+                skip_tools = 'baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools'
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --aligner bwa-mem --save_reference --build_only_index") {
+
+        when {
+            params {
+                aligner = 'bwa-mem'
+                build_only_index = true
+                input = false
+                outdir = "$outputDir"
+                save_reference = true
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/aligner-bwa-mem.nf.test.snap b/tests/aligner-bwa-mem.nf.test.snap
new file mode 100644
index 0000000000..633476af8b
--- /dev/null
+++ b/tests/aligner-bwa-mem.nf.test.snap
@@ -0,0 +1,118 @@
+{
+    "Run with profile test | --aligner bwa-mem --save_reference | skip QC/recal/md": {
+        "content": [
+            10,
+            {
+                "BAM_TO_CRAM_MAPPING": {
+                    "samtools": 1.21
+                },
+                "BWAMEM1_MEM": {
+                    "bwa": "0.7.18-r1243-dirty",
+                    "samtools": 1.2
+                },
+                "INDEX_MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "csv/mapped.csv",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "preprocessing",
+                "preprocessing/mapped",
+                "preprocessing/mapped/test",
+                "preprocessing/mapped/test/test.sorted.cram",
+                "preprocessing/mapped/test/test.sorted.cram.crai",
+                "reference",
+                "reference/bwa",
+                "reference/bwa/genome.amb",
+                "reference/bwa/genome.ann",
+                "reference/bwa/genome.bwt",
+                "reference/bwa/genome.pac",
+                "reference/bwa/genome.sa",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "test.sorted.cram:md5,9b21ccf9b5c61996bf48ce9dc0a108c5",
+                "test.sorted.cram.crai:md5,169697ea55e0749cc4d8312c32d73946",
+                "genome.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.bwt:md5,815eded87e4cb6b0f1daab5c4d6e30af",
+                "genome.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "genome.sa:md5,e7cff62b919448a3a3d0fe4aaf427594",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:17:55.189941"
+    },
+    "Run with profile test | --aligner bwa-mem --save_reference --build_only_index": {
+        "content": [
+            6,
+            {
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reference/bwa",
+                "reference/bwa/genome.amb",
+                "reference/bwa/genome.ann",
+                "reference/bwa/genome.bwt",
+                "reference/bwa/genome.pac",
+                "reference/bwa/genome.sa",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "genome.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.bwt:md5,815eded87e4cb6b0f1daab5c4d6e30af",
+                "genome.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "genome.sa:md5,e7cff62b919448a3a3d0fe4aaf427594",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:18:42.438866"
+    }
+}
\ No newline at end of file
diff --git a/tests/aligner-bwa-mem2.nf.test b/tests/aligner-bwa-mem2.nf.test
new file mode 100644
index 0000000000..6e752541cc
--- /dev/null
+++ b/tests/aligner-bwa-mem2.nf.test
@@ -0,0 +1,74 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --aligner bwa-mem2 --save_reference | skip QC/recal/md") {
+
+        when {
+            params {
+                aligner = 'bwa-mem2'
+                outdir = "$outputDir"
+                save_reference = true
+                skip_tools = 'baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools'
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --aligner bwa-mem2 --save_reference --build_only_index") {
+
+        when {
+            params {
+                aligner = 'bwa-mem2'
+                build_only_index = true
+                input = false
+                outdir = "$outputDir"
+                save_reference = true
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/aligner-bwa-mem2.nf.test.snap b/tests/aligner-bwa-mem2.nf.test.snap
new file mode 100644
index 0000000000..ae6b2466c3
--- /dev/null
+++ b/tests/aligner-bwa-mem2.nf.test.snap
@@ -0,0 +1,118 @@
+{
+    "Run with profile test | --aligner bwa-mem2 --save_reference --build_only_index": {
+        "content": [
+            6,
+            {
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reference/bwamem2",
+                "reference/bwamem2/genome.fasta.0123",
+                "reference/bwamem2/genome.fasta.amb",
+                "reference/bwamem2/genome.fasta.ann",
+                "reference/bwamem2/genome.fasta.bwt.2bit.64",
+                "reference/bwamem2/genome.fasta.pac",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
+                "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
+                "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:24:11.560414"
+    },
+    "Run with profile test | --aligner bwa-mem2 --save_reference | skip QC/recal/md": {
+        "content": [
+            10,
+            {
+                "BAM_TO_CRAM_MAPPING": {
+                    "samtools": 1.21
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.19.2"
+                },
+                "INDEX_MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "csv/mapped.csv",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "preprocessing",
+                "preprocessing/mapped",
+                "preprocessing/mapped/test",
+                "preprocessing/mapped/test/test.sorted.cram",
+                "preprocessing/mapped/test/test.sorted.cram.crai",
+                "reference",
+                "reference/bwamem2",
+                "reference/bwamem2/genome.fasta.0123",
+                "reference/bwamem2/genome.fasta.amb",
+                "reference/bwamem2/genome.fasta.ann",
+                "reference/bwamem2/genome.fasta.bwt.2bit.64",
+                "reference/bwamem2/genome.fasta.pac",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "test.sorted.cram:md5,47d93e48e806bbca9b76a72671c31256",
+                "test.sorted.cram.crai:md5,70f3ec29d6f6fc2d9fa87ada23cc3ec6",
+                "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
+                "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
+                "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:23:26.446846"
+    }
+}
\ No newline at end of file
diff --git a/tests/aligner-dragmap.nf.test b/tests/aligner-dragmap.nf.test
new file mode 100644
index 0000000000..707079feb5
--- /dev/null
+++ b/tests/aligner-dragmap.nf.test
@@ -0,0 +1,74 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --aligner dragmap --save_reference | skip QC/recal/md") {
+
+        when {
+            params {
+                aligner = 'dragmap'
+                outdir = "$outputDir"
+                save_reference = true
+                skip_tools = 'baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools'
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --aligner dragmap --save_reference --build_only_index") {
+
+        when {
+            params {
+                aligner = 'dragmap'
+                build_only_index = true
+                input = false
+                outdir = "$outputDir"
+                save_reference = true
+                tools = ''
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    getRelativePath(stable_name, outputDir),
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/aligner-dragmap.nf.test.snap b/tests/aligner-dragmap.nf.test.snap
new file mode 100644
index 0000000000..fe2a1f1820
--- /dev/null
+++ b/tests/aligner-dragmap.nf.test.snap
@@ -0,0 +1,131 @@
+{
+    "Run with profile test | --aligner dragmap --save_reference --build_only_index": {
+        "content": [
+            6,
+            {
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reference/dragmap",
+                "reference/dragmap/hash_table.cfg",
+                "reference/dragmap/hash_table.cfg.bin",
+                "reference/dragmap/hash_table.cmp",
+                "reference/dragmap/hash_table_stats.txt",
+                "reference/dragmap/ref_index.bin",
+                "reference/dragmap/reference.bin",
+                "reference/dragmap/repeat_mask.bin",
+                "reference/dragmap/str_table.bin",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "hash_table.cfg:md5,3bcf6daeb6548001513c676b0d368eb8",
+                "hash_table.cfg.bin:md5,13a07c5d7e7f2b41f4a3df5c09538883",
+                "hash_table.cmp:md5,1caab4ffc89f81ace615a2e813295cf4",
+                "hash_table_stats.txt:md5,94a7c3f9e157afeacc181ca78003d74f",
+                "ref_index.bin:md5,dbb5c7d26b974e0ac338024fe4535044",
+                "reference.bin:md5,be67b80ee48aa96b383fd72f1ccfefea",
+                "repeat_mask.bin:md5,294939f1f80aa7f4a70b9b537e4c0f21",
+                "str_table.bin:md5,45f7818c4a10fdeed04db7a34b5f9ff1",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:26:47.192744"
+    },
+    "Run with profile test | --aligner dragmap --save_reference | skip QC/recal/md": {
+        "content": [
+            10,
+            {
+                "BAM_TO_CRAM_MAPPING": {
+                    "samtools": 1.21
+                },
+                "DRAGMAP_ALIGN": {
+                    "dragmap": "1.2.1",
+                    "samtools": "1.19.2",
+                    "pigz": "2.3.4"
+                },
+                "INDEX_MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "MERGE_BAM": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "csv/mapped.csv",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "preprocessing",
+                "preprocessing/mapped",
+                "preprocessing/mapped/test",
+                "preprocessing/mapped/test/test.sorted.cram",
+                "preprocessing/mapped/test/test.sorted.cram.crai",
+                "reference",
+                "reference/dragmap",
+                "reference/dragmap/hash_table.cfg",
+                "reference/dragmap/hash_table.cfg.bin",
+                "reference/dragmap/hash_table.cmp",
+                "reference/dragmap/hash_table_stats.txt",
+                "reference/dragmap/ref_index.bin",
+                "reference/dragmap/reference.bin",
+                "reference/dragmap/repeat_mask.bin",
+                "reference/dragmap/str_table.bin",
+                "reference/intervals",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
+                "reference/intervals/genome.bed",
+                "reference/intervals/genome.bed.gz"
+            ],
+            [
+                "test.sorted.cram:md5,b9aba43d1397b9dee97f908a156710fa",
+                "test.sorted.cram.crai:md5,d59d42b04cd6482318d55bce388a9dca",
+                "hash_table.cfg:md5,8250732ed56bbfb714e45148cf090269",
+                "hash_table.cfg.bin:md5,0d5289f9840454d10eff0c0d5b207000",
+                "hash_table.cmp:md5,1caab4ffc89f81ace615a2e813295cf4",
+                "hash_table_stats.txt:md5,9985cfa1c9a5cd982019be82b3444af7",
+                "ref_index.bin:md5,dbb5c7d26b974e0ac338024fe4535044",
+                "reference.bin:md5,be67b80ee48aa96b383fd72f1ccfefea",
+                "repeat_mask.bin:md5,294939f1f80aa7f4a70b9b537e4c0f21",
+                "str_table.bin:md5,45f7818c4a10fdeed04db7a34b5f9ff1",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "genome.bed:md5,a87dc7d20ebca626f65cc16ff6c97a3e",
+                "genome.bed.gz:md5,a87dc7d20ebca626f65cc16ff6c97a3e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-07T10:25:59.685694"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index 56b247bfa3..6cddf47ad3 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -124,33 +124,6 @@ fastp:
 
 ## aligner
 
-### bwamem
-bwamem:
-  - conf/modules/aligner.config
-  - modules/nf-core/bwa/mem/**
-  - modules/nf-core/mosdepth/**
-  - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
-  - tests/csv/3.0/fastq_single.csv
-  - tests/test_aligner_bwamem.yml
-
-### bwamem2
-bwamem2:
-  - conf/modules/aligner.config
-  - modules/nf-core/bwamem2/mem/**
-  - modules/nf-core/mosdepth/**
-  - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
-  - tests/csv/3.0/fastq_single.csv
-  - tests/test_aligner_bwamem2.yml
-
-### dragmap
-dragmap:
-  - conf/modules/aligner.config
-  - modules/nf-core/dragmap/align/**
-  - modules/nf-core/mosdepth/**
-  - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
-  - tests/csv/3.0/fastq_single.csv
-  - tests/test_aligner_dragmap.yml
-
 ### sentieon/bwamem
 sentieon/bwamem:
   - conf/modules/aligner.config
diff --git a/tests/main.nf.test b/tests/default.nf.test
similarity index 100%
rename from tests/main.nf.test
rename to tests/default.nf.test
diff --git a/tests/main.nf.test.snap b/tests/default.nf.test.snap
similarity index 100%
rename from tests/main.nf.test.snap
rename to tests/default.nf.test.snap
diff --git a/tests/test_aligner_bwamem.yml b/tests/test_aligner_bwamem.yml
deleted file mode 100644
index ccd81021ef..0000000000
--- a/tests/test_aligner_bwamem.yml
+++ /dev/null
@@ -1,81 +0,0 @@
-- name: Run bwamem
-  command: nextflow run main.nf -profile test --aligner bwa-mem --save_reference --outdir results
-  tags:
-    - aligner
-    - bwamem
-    - preprocessing
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
-    - path: results/multiqc
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recal_table/test/test.recal.table
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns
-    - path: results/reference/bwa/genome.amb
-      md5sum: 1891c1de381b3a96d4e72f590fde20c1
-    - path: results/reference/bwa/genome.ann
-      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
-    - path: results/reference/bwa/genome.bwt
-      md5sum: 815eded87e4cb6b0f1daab5c4d6e30af
-    - path: results/reference/bwa/genome.pac
-      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
-    - path: results/reference/bwa/genome.sa
-      md5sum: e7cff62b919448a3a3d0fe4aaf427594
-    - path: results/reference/intervals/chr22_1-40001.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: results/reference/intervals/chr22_1-40001.bed.gz
-      md5sum: d3341fa28986c40b24fcc10a079dbb80
-    - path: results/reference/intervals/genome.bed
-      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["test	17094	1534	168	1046782	12429	197	0	0.635998", "1.0	0.999991	1171"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-    - path: results/reports/samtools/test/test.md.cram.stats
-    # conda changes md5sums for test
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test
-- name: Build only index with bwa
-  command: nextflow run main.nf -profile test --build_only_index --input false --outdir results
-  tags:
-    - aligner
-    - build_only_index
-    - bwamem
-  files:
-    - path: results/multiqc
-    - path: results/reference/bwa/genome.amb
-      md5sum: 1891c1de381b3a96d4e72f590fde20c1
-    - path: results/reference/bwa/genome.ann
-      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
-    - path: results/reference/bwa/genome.bwt
-      md5sum: 815eded87e4cb6b0f1daab5c4d6e30af
-    - path: results/reference/bwa/genome.pac
-      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
-    - path: results/reference/bwa/genome.sa
-      md5sum: e7cff62b919448a3a3d0fe4aaf427594
-    - path: results/reference/intervals/chr22_1-40001.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: results/reference/intervals/chr22_1-40001.bed.gz
-      md5sum: d3341fa28986c40b24fcc10a079dbb80
-    - path: results/reference/intervals/genome.bed
-      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
diff --git a/tests/test_aligner_bwamem2.yml b/tests/test_aligner_bwamem2.yml
deleted file mode 100644
index be19c08df6..0000000000
--- a/tests/test_aligner_bwamem2.yml
+++ /dev/null
@@ -1,81 +0,0 @@
-- name: Run bwamem2
-  command: nextflow run main.nf -profile test --aligner bwa-mem2 --save_reference --outdir results
-  tags:
-    - aligner
-    - bwamem2
-    - preprocessing
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
-    - path: results/multiqc
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recal_table/test/test.recal.table
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns
-    - path: results/reference/bwamem2/genome.fasta.0123
-      md5sum: d73300d44f733bcdb7c988fc3ff3e3e9
-    - path: results/reference/bwamem2/genome.fasta.amb
-      md5sum: 1891c1de381b3a96d4e72f590fde20c1
-    - path: results/reference/bwamem2/genome.fasta.ann
-      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
-    - path: results/reference/bwamem2/genome.fasta.bwt.2bit.64
-      md5sum: cd4bdf496eab05228a50c45ee43c1ed0
-    - path: results/reference/bwamem2/genome.fasta.pac
-      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
-    - path: results/reference/intervals/chr22_1-40001.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: results/reference/intervals/chr22_1-40001.bed.gz
-      md5sum: d3341fa28986c40b24fcc10a079dbb80
-    - path: results/reference/intervals/genome.bed
-      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["test	17094	1534	168	1046782	12429	197	0	0.635998", "1.0	0.999991	1171"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-    - path: results/reports/samtools/test/test.md.cram.stats
-    # conda changes md5sums for test
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test
-- name: Build only index with bwa-mem2
-  command: nextflow run main.nf -profile test --build_only_index --aligner bwa-mem2 --input false --outdir results
-  tags:
-    - aligner
-    - build_only_index
-    - bwamem2
-  files:
-    - path: results/multiqc
-    - path: results/reference/bwamem2/genome.fasta.0123
-      md5sum: d73300d44f733bcdb7c988fc3ff3e3e9
-    - path: results/reference/bwamem2/genome.fasta.amb
-      md5sum: 1891c1de381b3a96d4e72f590fde20c1
-    - path: results/reference/bwamem2/genome.fasta.ann
-      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
-    - path: results/reference/bwamem2/genome.fasta.bwt.2bit.64
-      md5sum: cd4bdf496eab05228a50c45ee43c1ed0
-    - path: results/reference/bwamem2/genome.fasta.pac
-      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
-    - path: results/reference/intervals/chr22_1-40001.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: results/reference/intervals/chr22_1-40001.bed.gz
-      md5sum: d3341fa28986c40b24fcc10a079dbb80
-    - path: results/reference/intervals/genome.bed
-      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
diff --git a/tests/test_aligner_dragmap.yml b/tests/test_aligner_dragmap.yml
deleted file mode 100644
index 6f38538926..0000000000
--- a/tests/test_aligner_dragmap.yml
+++ /dev/null
@@ -1,107 +0,0 @@
-- name: Run dragmap
-  command: nextflow run main.nf -profile test --aligner dragmap --save_reference --outdir results
-  tags:
-    - aligner
-    - dragmap
-    - preprocessing
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
-    - path: results/multiqc
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recal_table/test/test.recal.table
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns
-    - path: results/reference/dragmap/hash_table.cfg
-      contains:
-        [
-          "reference_sequences  = 1",
-          "reference_len        = 368640",
-          "reference_len_raw    = 40001",
-          "reference_len_not_n  = 40001",
-          "reference_alt_seed   = 204800",
-        ]
-    - path: results/reference/dragmap/hash_table.cfg.bin
-    # binary changes md5sums on reruns
-    - path: results/reference/dragmap/hash_table.cmp
-      md5sum: 1caab4ffc89f81ace615a2e813295cf4
-    - path: results/reference/dragmap/hash_table_stats.txt
-      contains: ["A bases:       10934", "C bases:        8612", "G bases:        8608", "T bases:       11847"]
-    - path: results/reference/dragmap/ref_index.bin
-      md5sum: dbb5c7d26b974e0ac338024fe4535044
-    - path: results/reference/dragmap/reference.bin
-      md5sum: be67b80ee48aa96b383fd72f1ccfefea
-    - path: results/reference/dragmap/repeat_mask.bin
-      md5sum: 294939f1f80aa7f4a70b9b537e4c0f21
-    - path: results/reference/dragmap/str_table.bin
-      md5sum: 45f7818c4a10fdeed04db7a34b5f9ff1
-    - path: results/reference/intervals/chr22_1-40001.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: results/reference/intervals/chr22_1-40001.bed.gz
-      md5sum: d3341fa28986c40b24fcc10a079dbb80
-    - path: results/reference/intervals/genome.bed
-      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["LB0	27214	1086	322	1037558	20017	100	0	0.687981"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-    - path: results/reports/samtools/test/test.md.cram.stats
-    # conda changes md5sums for test
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test
-- name: Build only index with dragmap
-  command: nextflow run main.nf -profile test --build_only_index --aligner dragmap --input false --outdir results
-  tags:
-    - aligner
-    - build_only_index
-    - dragmap
-  files:
-    - path: results/multiqc
-    - path: results/reference/dragmap/hash_table.cfg
-      contains:
-        [
-          "reference_sequences  = 1",
-          "reference_len        = 368640",
-          "reference_len_raw    = 40001",
-          "reference_len_not_n  = 40001",
-          "reference_alt_seed   = 204800",
-        ]
-    - path: results/reference/dragmap/hash_table.cfg.bin
-    # binary changes md5sums on reruns
-    - path: results/reference/dragmap/hash_table.cmp
-      md5sum: 1caab4ffc89f81ace615a2e813295cf4
-    - path: results/reference/dragmap/hash_table_stats.txt
-      contains: ["A bases:       10934", "C bases:        8612", "G bases:        8608", "T bases:       11847"]
-    - path: results/reference/dragmap/ref_index.bin
-      md5sum: dbb5c7d26b974e0ac338024fe4535044
-    - path: results/reference/dragmap/reference.bin
-      md5sum: be67b80ee48aa96b383fd72f1ccfefea
-    - path: results/reference/dragmap/repeat_mask.bin
-      md5sum: 294939f1f80aa7f4a70b9b537e4c0f21
-    - path: results/reference/dragmap/str_table.bin
-      md5sum: 45f7818c4a10fdeed04db7a34b5f9ff1
-    - path: results/reference/intervals/chr22_1-40001.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: results/reference/intervals/chr22_1-40001.bed.gz
-      md5sum: d3341fa28986c40b24fcc10a079dbb80
-    - path: results/reference/intervals/genome.bed
-      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e