diff --git a/modules/nf-core/angsd/dosaf/environment.yml b/modules/nf-core/angsd/dosaf/environment.yml
new file mode 100644
index 000000000000..2e83f3f2ca8f
--- /dev/null
+++ b/modules/nf-core/angsd/dosaf/environment.yml
@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::angsd=0.940
+  - bioconda::htslib=1.23
diff --git a/modules/nf-core/angsd/dosaf/main.nf b/modules/nf-core/angsd/dosaf/main.nf
new file mode 100644
index 000000000000..14ceb77fbd2d
--- /dev/null
+++ b/modules/nf-core/angsd/dosaf/main.nf
@@ -0,0 +1,137 @@
+process ANGSD_DOSAF {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/angsd:0.940--h13024bc_4':
+        'quay.io/biocontainers/angsd:0.940--h13024bc_4' }"
+
+    input:
+    tuple val(meta), path(bams), path(bam_indices)
+    tuple path(reference_fasta), path(reference_fai)
+    tuple path(ancestral_fasta), path(ancestral_fai) // Optional. Provides ancestral state for unfolded SFS.
+    path(error_file) // Optional. Required for SYK model (-GL 4) only.
+    path(inbreeding_coefficients) // Optional. Required for -doSAF 2 (inbreeding-aware mode).
+    val(gl_model)
+    val(dosaf_mode)
+
+    output:
+    tuple val(meta), path("*.saf.idx"), path("*.saf.pos.gz"), path("*.saf.gz"), emit: saf
+    tuple val("${task.process}"), val('angsd'), eval("angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'"), emit: versions_angsd, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // Validate GL model
+    if (!(gl_model in [1, 2, 3, 4])) {
+        error(
+            "ANGSD_DOSAF: Invalid GL model '${gl_model}'. Please pass one of 1, 2, 3, or 4 as the gl_model input."
+            )
+    }
+
+    // Validate doSAF mode
+    if (!(dosaf_mode in [1, 2])) {
+        error(
+            "ANGSD_DOSAF: Invalid doSAF mode '${dosaf_mode}'. Please pass 1 or 2 as the dosaf_mode input."
+            )
+    }
+
+    // Validate doSAF 2 has inbreeding coefficients
+    if (dosaf_mode == 2 && !inbreeding_coefficients) {
+        error(
+            "ANGSD_DOSAF: -doSAF 2 requires inbreeding coefficients (indF). Please supply an inbreeding_coefficients file."
+            )
+    }
+
+    // Validate doSAF 2 called alongside -doMajoMinor and -doMaf
+    if (dosaf_mode == 2 && !(args.contains("-doMajorMinor"))) {
+        error(
+            "ANGSD_DOSAF: -doSAF 2 requires -doMajorMinor to be specified. Please include in ext.args."
+            )
+    }
+    if (dosaf_mode == 2 && !(args.contains("-doMaf"))) {
+        error(
+            "ANGSD_DOSAF: -doSAF 2 requires -doMaf to be specified. Please include in ext.args."
+            )
+    }
+
+    // Validate GL 4 has error file
+    if (gl_model == 4 && !error_file) {
+        error(
+            "ANGSD_DOSAF: -GL 4 (SYK model) requires an error file. Please supply an error_file."
+            )
+    }
+
+    // Compute -minInd dynamically as a fraction of the population's BAM list size
+    // Default set to 0 as this mimics angsd default for minInd
+    def frac        = (task.ext.args2 ?: '0') as Double
+    def n_samples   = bams instanceof List ? bams.size() : 1
+    def min_ind_arg = frac > 0 ? "-minInd ${Math.ceil(n_samples * frac).toInteger()}" : ''
+
+    // Touch fai indices to ensure they are newer than their fasta (ANGSD requirement)
+    def touch_ref = reference_fai  ? "sleep 1 && touch ${reference_fai}"  : ''
+    def touch_anc = ancestral_fai  ? "sleep 1 && touch ${ancestral_fai}"  : ''
+
+    // Reference / ancestral args.
+    // If ancestral_fasta supplied: use as -anc and pass reference as -ref.
+    // If not supplied: use reference as -anc and -ref (suitable for folded SFS via realSFS -fold 1).
+    def ref_anc_arg = ancestral_fasta ? "-anc ${ancestral_fasta} -ref ${reference_fasta}" : "-anc ${reference_fasta} -ref ${reference_fasta}"
+
+    // Optional args
+    def indF_arg   = inbreeding_coefficients ? "-indF ${inbreeding_coefficients}" : ""
+    def errors_arg = error_file              ? "-errors ${error_file}"            : ""
+
+    // Shared preamble
+    def preamble = """
+    ${touch_ref}
+    ${touch_anc}
+    printf '%s\\n' ${bams} > bamlist.txt
+    """
+
+// SOAPsnp (-GL 3) needs a calibration pass first to generate the matrix
+// angsd reads back in during the doSAF step.
+def calibration = ''
+if (gl_model == 3) {
+    calibration = """
+    angsd \\
+        -nThreads ${task.cpus} \\
+        -bam bamlist.txt \\
+        -minQ 0 \\
+        -GL ${gl_model} \\
+        -ref ${reference_fasta} \\
+        -out ${prefix}
+    """
+}
+
+// SYK model (-GL 4) needs an error file and -doCounts 1
+def gl4_args = gl_model == 4 ? "${errors_arg} -doCounts 1" : ''
+
+"""
+${preamble}
+${calibration}
+angsd \\
+    -nThreads ${task.cpus} \\
+    -bam bamlist.txt \\
+    -GL ${gl_model} \\
+    -doSAF ${dosaf_mode} \\
+    ${ref_anc_arg} \\
+    ${indF_arg} \\
+    ${gl4_args} \\
+    ${args} \\
+    ${min_ind_arg} \\
+    -out ${prefix}
+"""
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.saf.idx
+    echo "" | gzip > ${prefix}.saf.pos.gz
+    echo "" | gzip > ${prefix}.saf.gz
+    """
+}
diff --git a/modules/nf-core/angsd/dosaf/meta.yml b/modules/nf-core/angsd/dosaf/meta.yml
new file mode 100644
index 000000000000..d62fe6724dae
--- /dev/null
+++ b/modules/nf-core/angsd/dosaf/meta.yml
@@ -0,0 +1,131 @@
+name: "angsd_dosaf"
+description: Estimate site allele frequencies from BAM files.
+keywords:
+  - angsd
+  - genotype likelihood
+  - genomics
+tools:
+  - "angsd":
+      description: "ANGSD: Analysis of next generation Sequencing Data"
+      homepage: "http://www.popgen.dk/angsd/"
+      documentation: "http://www.popgen.dk/angsd/"
+      tool_dev_url: "https://github.com/ANGSD/angsd"
+      doi: "10.1186/s12859-014-0356-4"
+      licence:
+        - "GPL v3"
+        - "MIT"
+      identifier: biotools:angsd
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing population information
+          e.g. [ id:'test', population:'population id', samples:'sample IDs' ]
+    - bams:
+        type: file
+        description: A list of BAM or CRAM files.
+        pattern: "*.{bam,cram}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572"
+          - edam: "http://edamontology.org/format_3462"
+    - bam_indices:
+        type: file
+        description: A list of BAM or CRAM indices.
+        pattern: "*.{bam.bai,cram.crai}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3327"
+          - edam: "http://edamontology.org/format_3462"
+  - - reference_fasta:
+        type: file
+        description: A reference genome in FASTA format.
+        pattern: "*.{fasta,fa,fasta.gz,fa.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+    - reference_fai:
+        type: file
+        description: Index of the reference genome FASTA file.
+        pattern: "*.{fasta,fa,fasta.gz,fa.gz}.fai"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+  - - ancestral_fasta:
+        type: file
+        description: An ancestral state genome in FASTA format.
+        pattern: "*.{fasta,fa,fasta.gz,fa.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+    - ancestral_fai:
+        type: file
+        description: Index of the ancestral state genome FASTA file.
+        pattern: "*.{fasta,fa,fasta.gz,fa.gz}.fai"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929" 
+  - error_file:
+      type: file
+      description: A file containing per-base substitution error rates for use
+        with the Sykes genotype likelihood model (-GL 4).
+      pattern: "*.errors"
+      ontologies: []
+  - inbreeding_coefficients:
+      type: file
+      description: A file containing estimates of individual inbreeding
+        coefficients.
+      pattern: "*.indF"
+      ontologies: []
+  - gl_model:
+      type: integer
+      description: |
+        Genotype likelihood model to use (angsd -GL). 1=SAMtools, 2=GATK, 3=SOAPsnp, 4=SYK.
+  - dosaf_mode:
+      type: integer
+      description: |
+        Site allele frequency likelihood estimation mode (angsd -doSAF). 1=standard, 2=inbreeding-aware (requires indF).
+output:
+  saf:
+    - - meta:
+          type: map
+          description: Groovy Map containing population information. e.g. `[
+            id:'test', population:'population id', samples:'sample IDs' ]`
+      - "*.saf.idx":
+          type: file
+          description: ANGSD site allele frequency index file
+          pattern: "*.saf.idx"
+          ontologies: []
+      - "*.saf.pos.gz":
+          type: file
+          description: Gzipped file containing genomic positions of sites in the
+            SAF
+          pattern: "*.saf.pos.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989
+      - "*.saf.gz":
+          type: file
+          description: Gzipped binary file containing per-site sample allele
+            frequency likelihoods
+          pattern: "*.saf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989
+  versions_angsd:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - angsd:
+          type: string
+          description: The name of the tool
+      - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - angsd:
+          type: string
+          description: The name of the tool
+      - "angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@ASendellPrice"
+maintainers:
+  - "@ASendellPrice"
diff --git a/modules/nf-core/angsd/dosaf/tests/main.nf.test b/modules/nf-core/angsd/dosaf/tests/main.nf.test
new file mode 100644
index 000000000000..e8bf55d1a314
--- /dev/null
+++ b/modules/nf-core/angsd/dosaf/tests/main.nf.test
@@ -0,0 +1,843 @@
+nextflow_process {
+
+    name "Test Process ANGSD_DOSAF"
+    script "../main.nf"
+    process "ANGSD_DOSAF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "angsd"
+    tag "angsd/dosaf"
+
+
+    // -------------------------------------------------------------------------
+    // SUCCESS CASE 1: GL 1; doSAF 1; no ancestral
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL 1 - doSAF 1") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 1
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.saf },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // SUCCESS CASE 2: GL 1; doSAF 2; no ancestral
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL 1 - doSAF 2") {
+        config "./nextflow.config"
+
+        setup{
+            new File("${launchDir}/angsd_FIN.indF").text = "0.0\n0.0\n0.01\n0.017\n"
+        }
+
+        when {
+            params {
+                angsd_args   = '-doMajorMinor 1 -doMaf 1 -r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = file("${launchDir}/angsd_FIN.indF", checkIfExists: true)
+                input[5] = 1
+                input[6] = 2
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.saf },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // SUCCESS CASE 3: GL 3; doSAF 1; no ancestral
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL3 - two steps") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 3
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.saf },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // SUCCESS CASE 4: GL 4 (requires error file)
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL4") {
+        config "./nextflow.config"
+
+        setup {
+            new File("${launchDir}/angsd_syk.errors").text = "0.000000\t0.005488\t0.003847\t0.003137\t0.006807\t0.000000\t0.001972\t0.002396\t0.002190\t0.001855\t0.000000\t0.008068\t0.002491\t0.004268\t0.005812\t0.000000\n"
+        }
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = file("${launchDir}/angsd_syk.errors", checkIfExists: true)
+                input[4] = []
+                input[5] = 4
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.saf },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // SUCCESS CASE 5: GL 1; doSAF 1; with ancestral FASTA
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL 1 - doSAF 1 - with ancestral fasta") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/resources/homo_sapiens_ancestor_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/resources/homo_sapiens_ancestor_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[3] = []
+                input[4] = []
+                input[5] = 1
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.saf },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // SUCCESS CASE 6: GL 1; doSAF 1; min_ind_frac > 0
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL 1 - doSAF 1 - min_ind_frac") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0.5
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 1
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.saf },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // FAILURE CASE 1: Missing inbreeding coefficients file (needed for doSAF 2)
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL1 - doSAF2 - missing inbreeding coefficients") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 1
+                input[6] = 2
+                """
+            }
+        }
+
+        then {
+            def caused = process.errorReport
+                .split("Source block:")[0]
+                .split("Caused by:")[1]
+                .trim()
+
+            assertAll(
+                { assert process.failed },
+                { assert caused.contains("-doSAF 2 requires inbreeding coefficients") }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // FAILURE CASE 2: Missing doSAF mode (not supplied)
+    // -------------------------------------------------------------------------
+
+    test("angsd - missing doSAF mode") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 1
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            def caused = process.errorReport
+                .split("Source block:")[0]
+                .split("Caused by:")[1]
+                .trim()
+
+            assertAll(
+                { assert process.failed },
+                { assert caused.contains("Invalid doSAF mode") }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // FAILURE CASE 3: Missing GL model (not supplied)
+    // -------------------------------------------------------------------------
+
+    test("angsd - missing GL model") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            def caused = process.errorReport
+                .split("Source block:")[0]
+                .split("Caused by:")[1]
+                .trim()
+
+            assertAll(
+                { assert process.failed },
+                { assert caused.contains("Invalid GL model") }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // FAILURE CASE 4: Invalid GL value
+    // -------------------------------------------------------------------------
+
+    test("angsd - invalid -GL value") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 5
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            def caused = process.errorReport
+                .split("Source block:")[0]
+                .split("Caused by:")[1]
+                .trim()
+
+            assertAll(
+                { assert process.failed },
+                { assert caused.contains("Invalid GL model") }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // FAILURE CASE 5: Missing error file (required by -GL 4)
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL4 - missing error file") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {"""
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 4
+                input[6] = 1
+                """}
+        }
+
+        then {
+            def caused = process.errorReport
+                .split("Source block:")[0]
+                .split("Caused by:")[1]
+                .trim()
+
+            assertAll(
+                { assert process.failed },
+                { assert caused.contains("-GL 4 (SYK model) requires an error file") }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // FAILURE CASE 6: doSAF 2 called without -doMajorMinor
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL 1 - doSAF 2 - missing -doMajorMinor") {
+        config "./nextflow.config"
+
+        setup{
+            new File("${launchDir}/angsd_FIN.indF").text = "0.0\n0.0\n0.01\n0.017\n"
+        }
+
+        when {
+            params {
+                angsd_args   = '-doMaf 1 -r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = file("${launchDir}/angsd_FIN.indF", checkIfExists: true)
+                input[5] = 1
+                input[6] = 2
+                """
+            }
+        }
+
+        then {
+            def caused = process.errorReport
+                .split("Source block:")[0]
+                .split("Caused by:")[1]
+                .trim()
+
+            assertAll(
+                { assert process.failed },
+                { assert caused.contains("-doSAF 2 requires -doMajorMinor to be specified. Please include in ext.args.") }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // FAILURE CASE 7: doSAF 2 called without -doMaf
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL 1 - doSAF 2 - missing -doMaf") {
+        config "./nextflow.config"
+
+        setup{
+            new File("${launchDir}/angsd_FIN.indF").text = "0.0\n0.0\n0.01\n0.017\n"
+        }
+
+        when {
+            params {
+                angsd_args   = '-doMajorMinor 1 -r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = file("${launchDir}/angsd_FIN.indF", checkIfExists: true)
+                input[5] = 1
+                input[6] = 2
+                """
+            }
+        }
+
+        then {
+            def caused = process.errorReport
+                .split("Source block:")[0]
+                .split("Caused by:")[1]
+                .trim()
+
+            assertAll(
+                { assert process.failed },
+                { assert caused.contains("-doSAF 2 requires -doMaf to be specified. Please include in ext.args.") }
+            )
+        }
+    }
+
+
+    // -------------------------------------------------------------------------
+    // STUB
+    // -------------------------------------------------------------------------
+
+    test("angsd - GL 1 - doSAF 1 - stub") {
+        options "-stub"
+        config "./nextflow.config"
+
+        when {
+            params {
+                angsd_args   = '-r chr20:1400000-1500000 -checkBamHeaders 0'
+                min_ind_frac = 0
+            }
+            process {
+                """
+                input[0] = [
+                    [
+                        id: "FIN",
+                        population: "FIN",
+                        samples: ["HG00349", "HG00358", "HG00350", "HG00351"]
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam")
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00349.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00350.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00351.chr20_1400000-1500000.bam.bai"),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/HG00358.chr20_1400000-1500000.bam.bai")
+                    ]
+                ]
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz'),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr20/sequence/GRCh38_chr20_1_2000000.fasta.gz.fai')
+                ]
+                input[2] = [ [], [] ]
+                input[3] = []
+                input[4] = []
+                input[5] = 1
+                input[6] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/angsd/dosaf/tests/main.nf.test.snap b/modules/nf-core/angsd/dosaf/tests/main.nf.test.snap
new file mode 100644
index 000000000000..8394d92a34db
--- /dev/null
+++ b/modules/nf-core/angsd/dosaf/tests/main.nf.test.snap
@@ -0,0 +1,271 @@
+{
+    "angsd - GL 1 - doSAF 2": {
+        "content": [
+            {
+                "saf": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,f825a57ec037dd03127fced8c11c1f84",
+                        "FIN.saf.pos.gz:md5,bbdf128514097d6faa7c71031af7b97b",
+                        "FIN.saf.gz:md5,5b8d21df08479f96405d430758937977"
+                    ]
+                ],
+                "versions_angsd": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-16T12:41:01.480791",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "angsd - GL 1 - doSAF 1": {
+        "content": [
+            {
+                "saf": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,c2a21e30aacb59091931c3651ea69ccd",
+                        "FIN.saf.pos.gz:md5,bbdf128514097d6faa7c71031af7b97b",
+                        "FIN.saf.gz:md5,8ca7bbf4f93b7aa09cb6da8f7c87c132"
+                    ]
+                ],
+                "versions_angsd": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-16T12:40:55.726472",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "angsd - GL 1 - doSAF 1 - with ancestral fasta": {
+        "content": [
+            {
+                "saf": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,c2a21e30aacb59091931c3651ea69ccd",
+                        "FIN.saf.pos.gz:md5,bbdf128514097d6faa7c71031af7b97b",
+                        "FIN.saf.gz:md5,29eb0ee312740e0aa6de230e6405e44e"
+                    ]
+                ],
+                "versions_angsd": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-16T12:41:27.922853",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "angsd - GL3 - two steps": {
+        "content": [
+            {
+                "saf": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,ed87cdf671b5b11137b5082f05e3ce6a",
+                        "FIN.saf.pos.gz:md5,bbdf128514097d6faa7c71031af7b97b",
+                        "FIN.saf.gz:md5,095fc8b1763ae7be00218e0d52e1a1b4"
+                    ]
+                ],
+                "versions_angsd": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-16T12:41:15.856922",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "angsd - GL 1 - doSAF 1 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "FIN.saf.pos.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "FIN.saf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ],
+                "saf": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "FIN.saf.pos.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "FIN.saf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions_angsd": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-16T12:41:57.125426",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "angsd - GL4": {
+        "content": [
+            {
+                "saf": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,821d582655745d035cd963012e04684e",
+                        "FIN.saf.pos.gz:md5,bbdf128514097d6faa7c71031af7b97b",
+                        "FIN.saf.gz:md5,e21b7f5dfdcdeec7bd59a3c203a95c7c"
+                    ]
+                ],
+                "versions_angsd": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-16T12:41:21.255121",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    },
+    "angsd - GL 1 - doSAF 1 - min_ind_frac": {
+        "content": [
+            {
+                "saf": [
+                    [
+                        {
+                            "id": "FIN",
+                            "population": "FIN",
+                            "samples": [
+                                "HG00349",
+                                "HG00358",
+                                "HG00350",
+                                "HG00351"
+                            ]
+                        },
+                        "FIN.saf.idx:md5,4fc612eb149887c6238af1d4239ffc7e",
+                        "FIN.saf.pos.gz:md5,12f398f2c01708e40b32da38931ffd68",
+                        "FIN.saf.gz:md5,5692b34cf0807dcbb92eca36f970b975"
+                    ]
+                ],
+                "versions_angsd": [
+                    [
+                        "ANGSD_DOSAF",
+                        "angsd",
+                        "0.940-dirty"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-16T12:41:34.159609",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/angsd/dosaf/tests/nextflow.config b/modules/nf-core/angsd/dosaf/tests/nextflow.config
new file mode 100644
index 000000000000..10a06e4c1b6a
--- /dev/null
+++ b/modules/nf-core/angsd/dosaf/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: ANGSD_DOSAF {
+        ext.args  = { params.angsd_args }
+        ext.args2 = { params.min_ind_frac }
+    }
+}