diff --git a/modules.json b/modules.json
index 879d22a8..9cff4eec 100644
--- a/modules.json
+++ b/modules.json
@@ -16,6 +16,21 @@
                         "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
                         "installed_by": ["modules"]
                     },
+                    "opt/flip": {
+                        "branch": "master",
+                        "git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
+                        "installed_by": ["modules"]
+                    },
+                    "opt/stat": {
+                        "branch": "master",
+                        "git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
+                        "installed_by": ["modules"]
+                    },
+                    "opt/track": {
+                        "branch": "master",
+                        "git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
+                        "installed_by": ["modules"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
diff --git a/modules/nf-core/opt/flip/main.nf b/modules/nf-core/opt/flip/main.nf
new file mode 100644
index 00000000..fa98c4f0
--- /dev/null
+++ b/modules/nf-core/opt/flip/main.nf
@@ -0,0 +1,55 @@
+process OPT_FLIP {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "khersameesh24/opt:v0.0.1"
+
+    input:
+    tuple val(meta), path(probes_fasta)
+    tuple val(meta2), path(ref_annot_gff), path(ref_annot_fa)
+
+    output:
+    tuple val(meta), path("${meta.id}/fwd_oriented.fa"), emit: fwd_oriented_fa
+    path "versions.yml"                                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "OPT_FLIP module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    opt \\
+    -o ${prefix} \\
+    -p ${task.cpus} \\
+    flip \\
+    -q ${probes_fasta} \\
+    -a ${ref_annot_gff} \\
+    -t ${ref_annot_fa} \\
+    ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        opt: \$(opt --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    mkdir -p ${prefix}
+    touch "${prefix}/fwd_oriented.fa"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        opt: \$(opt --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/opt/flip/meta.yml b/modules/nf-core/opt/flip/meta.yml
new file mode 100644
index 00000000..f0e4c57c
--- /dev/null
+++ b/modules/nf-core/opt/flip/meta.yml
@@ -0,0 +1,68 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "opt_flip"
+description: "flip corrects probes that are aligning to the opposite strand of their intended target genes by reverse complementing them"
+keywords:
+  - opt
+  - opt flip
+  - transcripts
+  - off-target probes
+  - align probes
+tools:
+  - "opt":
+      description: "opt is a simple program that aligns probe sequences to transcript sequences to detect potential off-target probe activity"
+      homepage: "https://github.com/JEFworks-Lab/off-target-probe-tracker"
+      documentation: "https://github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md"
+      tool_dev_url: "https://github.com/JEFworks-Lab/off-target-probe-tracker"
+      licence: [GPL-3.0 license]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information of the probe panel sequences used for the xenium experiment
+          e.g. `[ id:'breast_cancer_probe_panel_sequences' ]`
+    - probes_fasta:
+        type: file
+        description: Fasta file for the probe sequences used in the xenium experiment
+        pattern: "*.fasta"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing the information of the genomic features and fasta files used as references
+          e.g. `[ id:'gencode_references' ]`
+    - ref_annot_gff:
+        type: file
+        description: Reference annotations in gff format
+        pattern: "*.gff"
+        ontologies: []
+    - ref_annot_fa:
+        type: file
+        description: Reference annotations in fasta format
+        pattern: "*.fa"
+        ontologies: []
+
+output:
+  fwd_oriented_fa:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences 'opt flip'
+            e.g. `[ id:'breast_cancer_probe_panel_sequences' ]`
+      - "${meta.id}/fwd_oriented.fa":
+          type: file
+          description: The forward oriented fasta file
+          pattern: "*.fa"
+          ontologies: []
+  versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/opt/flip/tests/main.nf.test b/modules/nf-core/opt/flip/tests/main.nf.test
new file mode 100644
index 00000000..77fd9ef4
--- /dev/null
+++ b/modules/nf-core/opt/flip/tests/main.nf.test
@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process OPT_FLIP"
+    script "../main.nf"
+    process "OPT_FLIP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "opt"
+    tag "opt/flip"
+
+    test("testrun panel probe sequences") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_run' ],
+                    file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/panel_probe_sequences.fasta', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test_run' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("testrun panel probe sequences -stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_run' ],
+                    file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/panel_probe_sequences.fasta', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test_run' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/opt/flip/tests/main.nf.test.snap b/modules/nf-core/opt/flip/tests/main.nf.test.snap
new file mode 100644
index 00000000..4bc5b35e
--- /dev/null
+++ b/modules/nf-core/opt/flip/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "testrun panel probe sequences -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "fwd_oriented.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,57dbc672cf0bf40854c18d241f2d7d2e"
+                ],
+                "fwd_oriented_fa": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "fwd_oriented.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,57dbc672cf0bf40854c18d241f2d7d2e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-14T12:43:08.105988801"
+    },
+    "testrun panel probe sequences": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "fwd_oriented.fa:md5,535289c04851ad94e091ec7c14ff6bcd"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,57dbc672cf0bf40854c18d241f2d7d2e"
+                ],
+                "fwd_oriented_fa": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "fwd_oriented.fa:md5,535289c04851ad94e091ec7c14ff6bcd"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,57dbc672cf0bf40854c18d241f2d7d2e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-14T12:47:41.966183182"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/opt/stat/main.nf b/modules/nf-core/opt/stat/main.nf
new file mode 100644
index 00000000..b4e2875e
--- /dev/null
+++ b/modules/nf-core/opt/stat/main.nf
@@ -0,0 +1,56 @@
+process OPT_STAT {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "khersameesh24/opt:v0.0.1"
+
+    input:
+    tuple val(meta), path(probe_targets)
+    tuple val(meta2), path(fwd_oriented_probes)
+    path(gene_synonyms)
+
+    output:
+    tuple val(meta), path("${meta.id}/collapsed_summary.tsv"), emit: summary
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "OPT_STAT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def synonyms = gene_synonyms ? "-s ${gene_synonyms}": ""
+
+    """
+    opt \\
+    -o ${prefix} \\
+    stat \\
+    -i ${probe_targets} \\
+    -q ${fwd_oriented_probes} \\
+    ${synonyms} \\
+    ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        opt: \$(opt --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}
+    touch "${prefix}/collapsed_summary.tsv"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        opt: \$(opt --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/opt/stat/meta.yml b/modules/nf-core/opt/stat/meta.yml
new file mode 100644
index 00000000..ae2d712b
--- /dev/null
+++ b/modules/nf-core/opt/stat/meta.yml
@@ -0,0 +1,72 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "opt_stat"
+description: "stat summarizes opt binding predictions"
+keywords:
+  - opt
+  - opt stat
+  - transcripts
+  - binding predictions
+  - off-target probes
+  - align probes
+  - summary stats
+tools:
+  - "opt":
+      description: "opt is a simple program that aligns probe sequences to transcript
+        sequences to detect potential off-target probe activity"
+      homepage: "https://github.com/JEFworks-Lab/off-target-probe-tracker"
+      documentation: "https://github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md"
+      tool_dev_url: "https://github.com/JEFworks-Lab/off-target-probe-tracker"
+      licence: [GPL-3.0 license]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing information of the probe targets generated from the panel sequences with `opt track`
+          e.g. `[ id:'breast_cancer_probe_panel_sequences' ]`
+    - probe_targets:
+        type: file
+        description: Generated probe targets
+        pattern: "*.tsv"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences 'opt flip'
+          e.g. `[ id:'breast_cancer_probe_panel_sequences' ]`
+    - fwd_oriented_probes:
+        type: file
+        description: The forward oriented fasta file
+        pattern: "*.fa"
+        ontologies: []
+  - gene_synonyms:
+      type: file
+      description: Gene synonyms that may have been counted as off-targets but
+        simply differ in name (optional input)
+      pattern: "*.csv"
+      ontologies: []
+output:
+  summary:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing summary of the forward oriented probes generated with the panel sequences 'opt flip and track'
+            e.g. `[ id:'breast_cancer_probe_panel_sequences' ]`
+      - "${meta.id}/collapsed_summary.tsv":
+          type: file
+          description: tsv file containing the summary stats
+          pattern: "*.tsv"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/opt/stat/tests/main.nf.test b/modules/nf-core/opt/stat/tests/main.nf.test
new file mode 100644
index 00000000..5204a81f
--- /dev/null
+++ b/modules/nf-core/opt/stat/tests/main.nf.test
@@ -0,0 +1,63 @@
+nextflow_process {
+
+    name "Test Process OPT_STAT"
+    script "../main.nf"
+    process "OPT_STAT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "opt"
+    tag "opt/stat"
+
+    test("testrun panel probe sequences") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_run' ],
+                    file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/probe2targets.tsv', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test_run' ],
+                    file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/fwd_oriented.fa', checkIfExists: true)
+                ]
+                input[2] = []
+                // input[2] = [file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/gene_synonyms.csv', checkIfExists: true)]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("testrun panel probe sequences -stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_run' ],
+                    file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/probe2targets.tsv', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test_run' ],
+                    file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/fwd_oriented.fa', checkIfExists: true)
+                ]
+                input[2] = []
+                // input[2] = [file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/gene_synonyms.csv', checkIfExists: true)]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/opt/stat/tests/main.nf.test.snap b/modules/nf-core/opt/stat/tests/main.nf.test.snap
new file mode 100644
index 00000000..b14671fe
--- /dev/null
+++ b/modules/nf-core/opt/stat/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "testrun panel probe sequences -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "collapsed_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a23b08ea3b2da18863a5611dd0adbaa1"
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "collapsed_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a23b08ea3b2da18863a5611dd0adbaa1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-14T12:23:32.959930982"
+    },
+    "testrun panel probe sequences": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "collapsed_summary.tsv:md5,b2884d9c8c89124d3cbbbc1223d81c99"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a23b08ea3b2da18863a5611dd0adbaa1"
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "collapsed_summary.tsv:md5,b2884d9c8c89124d3cbbbc1223d81c99"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a23b08ea3b2da18863a5611dd0adbaa1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-14T12:58:57.17786325"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/opt/track/main.nf b/modules/nf-core/opt/track/main.nf
new file mode 100644
index 00000000..fc99a3e5
--- /dev/null
+++ b/modules/nf-core/opt/track/main.nf
@@ -0,0 +1,56 @@
+process OPT_TRACK {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "khersameesh24/opt:v0.0.1"
+
+    input:
+    tuple val(meta), path(fwd_oriented_fa)
+    tuple val(meta2), path(ref_annot_gff), path(ref_annot_fa)
+
+    output:
+    tuple val(meta), path("${meta.id}/probe2targets.tsv"), emit: probes2target
+    path "versions.yml"                                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "OPT_TRACK module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    opt \\
+    -o ${prefix} \\
+    -p ${task.cpus} \\
+    track \\
+    -q ${fwd_oriented_fa} \\
+    -a ${ref_annot_gff} \\
+    -t ${ref_annot_fa} \\
+    ${args}
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        opt: \$(opt --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    mkdir -p ${prefix}
+    touch "${prefix}/probe2targets.tsv"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        opt: \$(opt --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/opt/track/meta.yml b/modules/nf-core/opt/track/meta.yml
new file mode 100644
index 00000000..6024d773
--- /dev/null
+++ b/modules/nf-core/opt/track/meta.yml
@@ -0,0 +1,69 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "opt_track"
+description: "track aligns query probe sequences to any target transcriptome"
+keywords:
+  - opt
+  - opt track
+  - transcripts
+  - off-target probes
+  - align probes
+  - traget transcriptome
+tools:
+  - "opt":
+      description: "opt is a simple program that aligns probe sequences to transcript sequences to detect potential off-target probe activity"
+      homepage: "https://github.com/JEFworks-Lab/off-target-probe-tracker"
+      documentation: "https://github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md"
+      tool_dev_url: "https://github.com/JEFworks-Lab/off-target-probe-tracker"
+      licence: [GPL-3.0 license]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences generated with `opt flip`
+          e.g. `[ id:'breast_cancer_probe_panel_sequences' ]`
+    - fwd_oriented_fa:
+        type: file
+        description: Forward oriented fasta file generated by the opt flip command
+        pattern: "*.fa"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing the information of the genomic features and fasta files used as references
+          e.g. `[ id:'gencode_references' ]`
+    - ref_annot_gff:
+        type: file
+        description: Reference annotation in gff format
+        pattern: "*.gff"
+        ontologies: []
+    - ref_annot_fa:
+        type: file
+        description: Reference annotation in fasta format
+        pattern: "*.fa"
+        ontologies: []
+
+output:
+  probes2target:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "${meta.id}/probe2targets.tsv":
+          type: file
+          description: TSV file containing the gene and transcript information to which each probe aligns
+          pattern: "*.tsv"
+          ontologies: []
+  versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/opt/track/tests/main.nf.test b/modules/nf-core/opt/track/tests/main.nf.test
new file mode 100644
index 00000000..4fbf9a19
--- /dev/null
+++ b/modules/nf-core/opt/track/tests/main.nf.test
@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process OPT_TRACK"
+    script "../main.nf"
+    process "OPT_TRACK"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "opt"
+    tag "opt/track"
+
+    test("testrun panel probe sequences") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_run' ], file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/fwd_oriented.fa', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test_run' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("testrun panel probe sequences -stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_run' ], file('https://raw.githubusercontent.com/khersameesh24/test-datasets/opt/testdata/fwd_oriented.fa', checkIfExists: true)
+                ]
+                
+                input[1] = [
+                    [ id:'test_run' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/opt/track/tests/main.nf.test.snap b/modules/nf-core/opt/track/tests/main.nf.test.snap
new file mode 100644
index 00000000..3dda7a91
--- /dev/null
+++ b/modules/nf-core/opt/track/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "testrun panel probe sequences -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "probe2targets.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,daf660f286a817fa0eed7703a5f65706"
+                ],
+                "probes2target": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "probe2targets.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,daf660f286a817fa0eed7703a5f65706"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-14T12:20:29.220245783"
+    },
+    "testrun panel probe sequences": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "probe2targets.tsv:md5,e15465df3845d7a6acf64dd3be04391b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,daf660f286a817fa0eed7703a5f65706"
+                ],
+                "probes2target": [
+                    [
+                        {
+                            "id": "test_run"
+                        },
+                        "probe2targets.tsv:md5,e15465df3845d7a6acf64dd3be04391b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,daf660f286a817fa0eed7703a5f65706"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-14T12:20:19.999359259"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/opt_flip_track_stat/main.nf b/subworkflows/local/opt_flip_track_stat/main.nf
new file mode 100644
index 00000000..66272ef9
--- /dev/null
+++ b/subworkflows/local/opt_flip_track_stat/main.nf
@@ -0,0 +1,38 @@
+include { OPT_FLIP  } from '../../../modules/nf-core/opt/flip/main'
+include { OPT_TRACK } from '../../../modules/nf-core/opt/track/main'
+include { OPT_STAT  } from '../../../modules/nf-core/opt/stat/main'
+
+
+workflow OPT_FLIP_TRACK_STAT {
+
+    take:
+
+    ch_probe_fasta   // channel: [ val(meta), [ "panel_probes_sequences.fasta" ] ]
+    ch_references    // channel: [ val(meta), ["reference_annotations.gff"], ["reference_annotations.fa"] ]
+    ch_gene_synonyms // channel: [ "path-to-gene-synonyms" ]
+
+    main:
+
+    ch_versions = Channel.empty()
+    ch_summary  = Channel.empty()
+
+    // correct probes that are aligning to opposite strand with `flip`
+    OPT_FLIP ( ch_probe_fasta, ch_references )
+    ch_versions = ch_versions.mix( OPT_FLIP.out.versions )
+
+    // align query probe sequences to target transcriptome
+    OPT_TRACK ( OPT_FLIP.out.fwd_oriented_fa, ch_references )
+    ch_versions = ch_versions.mix( OPT_TRACK.out.versions )
+
+    // summarizes opt binding predictions
+    OPT_STAT ( OPT_TRACK.out.probes2target, OPT_FLIP.out.fwd_oriented_fa, ch_gene_synonyms )
+    ch_versions = ch_versions.mix( OPT_STAT.out.versions )
+
+    ch_summary = OPT_STAT.out.summary
+
+    emit:
+
+    summary = ch_summary    // channel: [ val(meta), ["collapsed_summary.tsv", "other-summary-files"]]
+
+    versions = ch_versions  // channel: [ versions.yml ]
+}
diff --git a/subworkflows/local/opt_flip_track_stat/meta.yml b/subworkflows/local/opt_flip_track_stat/meta.yml
new file mode 100644
index 00000000..07ccc8b7
--- /dev/null
+++ b/subworkflows/local/opt_flip_track_stat/meta.yml
@@ -0,0 +1,51 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "opt_flip_track_stat"
+description: opt is a simple program that aligns probe sequences to transcript sequences
+  to detect potential off-target probe activity
+keywords:
+  - opt
+  - flip
+  - track
+  - stat
+  - off-target probes
+components:
+  - opt/flip
+  - opt/track
+  - opt/stat
+input:
+  - ch_probe_fasta:
+      type: file
+      description: |
+        Input channel containing the sample info. and associated probe panel sequences fasta file
+        Structure: [ val(meta), path("porbe_panel_seqeunces.fasta") ]
+      pattern: "*.fasta"
+  - ch_references:
+      type: file
+      description: |
+        Input channel containing the sample info. and the references to be used
+        Structure: [ val(meta), path("reference_annotations.gff"), path("reference_annotations.fa") ]
+      pattern: "*.{fa,gff}"
+  - ch_gene_synonyms:
+      type: file
+      description: |
+        Input channel containing the Gene synonyms that may have been counted as off-targets but
+        simply differ in name (optional input)
+        Structure: [ val(meta), path("gene_synonyms.csv") ]
+      pattern: "*.csv"
+output:
+  - summary:
+      type: file
+      description: |
+        Groovy Map containing summary of the forward oriented probes generated with the panel sequences opt flip and track
+        Structure: [ val(meta), path("collapsed_summary.tsv") ]
+      pattern: "*.tsv"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"