diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml
new file mode 100644
index 00000000..114390be
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/environment.yml
@@ -0,0 +1,7 @@
+name: bcftools_mpileup
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
new file mode 100644
index 00000000..5e57644a
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/main.nf
@@ -0,0 +1,58 @@
+process BCFTOOLS_MPILEUP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(intervals)
+    tuple val(meta2), path(fasta)
+    val save_mpileup
+
+    output:
+    tuple val(meta), path("*vcf.gz")     , emit: vcf
+    tuple val(meta), path("*vcf.gz.tbi") , emit: tbi
+    tuple val(meta), path("*stats.txt")  , emit: stats
+    tuple val(meta), path("*.mpileup.gz"), emit: mpileup, optional: true
+    path  "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
+    def bgzip_mpileup = save_mpileup ? "bgzip ${prefix}.mpileup" : ""
+    def intervals = intervals ? "-T ${intervals}" : ""
+    """
+    echo "${meta.id}" > sample_name.list
+
+    bcftools \\
+        mpileup \\
+        --fasta-ref $fasta \\
+        $args \\
+        $bam \\
+        $intervals \\
+        $mpileup \\
+        | bcftools call --output-type v $args2 \\
+        | bcftools reheader --samples sample_name.list \\
+        | bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
+
+    $bgzip_mpileup
+
+    tabix -p vcf -f ${prefix}.vcf.gz
+
+    bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bcftools/mpileup/meta.yml b/modules/nf-core/bcftools/mpileup/meta.yml
new file mode 100644
index 00000000..65410ddd
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/meta.yml
@@ -0,0 +1,70 @@
+name: bcftools_mpileup
+description: Compresses VCF files
+keywords:
+  - variant calling
+  - mpileup
+  - VCF
+tools:
+  - mpileup:
+      description: |
+        Generates genotype likelihoods at each genomic position with coverage.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Input BAM file
+      pattern: "*.{bam}"
+  - intervals:
+      type: file
+      description: Input intervals file. A file (commonly '.bed') containing regions to subset
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information about the genome fasta, e.g. [ id: 'sarscov2' ]
+  - fasta:
+      type: file
+      description: FASTA reference file
+      pattern: "*.{fasta,fa}"
+  - save_mpileup:
+      type: boolean
+      description: Save mpileup file generated by bcftools mpileup
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF gzipped output file
+      pattern: "*.{vcf.gz}"
+  - tbi:
+      type: file
+      description: tabix index file
+      pattern: "*.{vcf.gz.tbi}"
+  - stats:
+      type: file
+      description: Text output file containing stats
+      pattern: "*{stats.txt}"
+  - mpileup:
+      type: file
+      description: mpileup gzipped output for all positions
+      pattern: "{*.mpileup.gz}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
diff --git a/modules/nf-core/bcftools/mpileup/tests/main.nf.test b/modules/nf-core/bcftools/mpileup/tests/main.nf.test
new file mode 100644
index 00000000..6478bbc2
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/main.nf.test
@@ -0,0 +1,116 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_MPILEUP"
+    script "../main.nf"
+    process "BCFTOOLS_MPILEUP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/mpileup"
+
+    config "./nextflow.config"
+
+    test("sarscov2 - [bam, []], fasta, false") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.tbi,
+                    process.out.stats,
+                    process.out.mpileup,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [bam, []], fasta, true") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.tbi,
+                    process.out.stats,
+                    process.out.mpileup,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [bam, bed], fasta, false") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.tbi,
+                    process.out.stats,
+                    process.out.mpileup,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap
new file mode 100644
index 00000000..ef80ab1b
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap
@@ -0,0 +1,112 @@
+{
+    "sarscov2 - [bam, []], fasta, true": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz:md5,0f2f2c8488e97e7f13979380d5d3b6b5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi:md5,34cb2eeb73f4d2b98218acecebd92704"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bcftools_stats.txt:md5,a988fbcd2ea5d1ce30970dcb60a77ed7"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.mpileup.gz:md5,73b4a00398bddab2cd065b40d17ca4dc"
+                ]
+            ],
+            [
+                "versions.yml:md5,e09c59d941374bb293aadc36e2f29dbf"
+            ]
+        ],
+        "timestamp": "2023-11-29T14:11:54.549517279"
+    },
+    "sarscov2 - [bam, bed], fasta, false": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz:md5,687244dbf71d05b3b973ab08ecf05310"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi:md5,3785df15f3d7faf35f3ad70d167a50f7"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bcftools_stats.txt:md5,f8c5ab149c4bf0e5f51c518346cb87b5"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,e09c59d941374bb293aadc36e2f29dbf"
+            ]
+        ],
+        "timestamp": "2023-11-29T14:12:00.865439661"
+    },
+    "sarscov2 - [bam, []], fasta, false": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz:md5,0f2f2c8488e97e7f13979380d5d3b6b5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi:md5,34cb2eeb73f4d2b98218acecebd92704"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bcftools_stats.txt:md5,a988fbcd2ea5d1ce30970dcb60a77ed7"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,e09c59d941374bb293aadc36e2f29dbf"
+            ]
+        ],
+        "timestamp": "2023-11-29T14:11:47.814900494"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/mpileup/tests/nextflow.config b/modules/nf-core/bcftools/mpileup/tests/nextflow.config
new file mode 100644
index 00000000..a7ba19fe
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/nextflow.config
@@ -0,0 +1,4 @@
+process {
+    ext.args2 = '--no-version --ploidy 1 --multiallelic-caller'
+    ext.args3 = '--no-version'
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/mpileup/tests/tags.yml b/modules/nf-core/bcftools/mpileup/tests/tags.yml
new file mode 100644
index 00000000..07b91f98
--- /dev/null
+++ b/modules/nf-core/bcftools/mpileup/tests/tags.yml
@@ -0,0 +1,2 @@
+bcftools/mpileup:
+  - "modules/nf-core/bcftools/mpileup/**"