diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6bd88ef5..7a2f87f2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -80,6 +80,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#451](https://github.com/genomic-medicine-sweden/nallo/pull/451) - Simplified methylation subworkflow
 - [#474](https://github.com/genomic-medicine-sweden/nallo/pull/474) - Updated VEP and CADD channels to fix bugs introduced in [#443](https://github.com/genomic-medicine-sweden/nallo/pull/443)
 - [#479](https://github.com/genomic-medicine-sweden/nallo/pull/479) - Replaced bgzip tabix with bcftools sort in rank variants to fix [#457](https://github.com/genomic-medicine-sweden/nallo/issues/457)
+- [#480](https://github.com/genomic-medicine-sweden/nallo/pull/480) - Updated ranking of SVs to work with multiple families per project
 - [#484](https://github.com/genomic-medicine-sweden/nallo/pull/484) - Updated metro map and added SVG version
 - [#487](https://github.com/genomic-medicine-sweden/nallo/pull/487) - Changed CI tests to only run tests where changes have been made
 
diff --git a/conf/modules/general.config b/conf/modules/general.config
index 92c504de..bcec5299 100644
--- a/conf/modules/general.config
+++ b/conf/modules/general.config
@@ -113,7 +113,14 @@ process {
 
     withName: '.*:NALLO:SOMALIER_PED' {
         publishDir = [
-            path: { "${params.outdir}/pedigree" },
+            path: { "${params.outdir}/pedigree/project/" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*:NALLO:SOMALIER_PED_FAMILY' {
+        publishDir = [
+            path: { "${params.outdir}/pedigree/family/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
diff --git a/docs/output.md b/docs/output.md
index 85de861f..11b8d461 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -121,12 +121,13 @@ If the pipeline is run with phasing, the aligned reads will be happlotagged usin
 
 [somalier](https://github.com/brentp/somalier) checks relatedness and sex.
 
-| Path                                                  | Description                                 |
-| ----------------------------------------------------- | ------------------------------------------- |
-| `pedigree/{project}.ped`                              | PED file updated with somalier-inferred sex |
-| `qc/somalier/relate/{project}/{project}.html`         | HTML report                                 |
-| `qc/somalier/relate/{project}/{project}.pairs.tsv`    | Information about sample pairs              |
-| `/qc/somalier/relate/{project}/{project}.samples.tsv` | Information about individual samples        |
+| Path                                                  | Description                                             |
+| ----------------------------------------------------- | ------------------------------------------------------- |
+| `pedigree/{project}/{project}.ped`                    | PED file updated with somalier-inferred sex per project |
+| `pedigree/{family}/{family).ped`                      | PED file updated with somalier-inferred sex per family  |
+| `qc/somalier/relate/{project}/{project}.html`         | HTML report                                             |
+| `qc/somalier/relate/{project}/{project}.pairs.tsv`    | Information about sample pairs                          |
+| `/qc/somalier/relate/{project}/{project}.samples.tsv` | Information about individual samples                    |
 
 | Path                      | Description                                 |
 | ------------------------- | ------------------------------------------- |
diff --git a/modules.json b/modules.json
index 9a4a3b04..4195dd68 100644
--- a/modules.json
+++ b/modules.json
@@ -114,12 +114,12 @@
                     },
                     "genmod/models": {
                         "branch": "master",
-                        "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c",
+                        "git_sha": "f888300c726e1f817a9f93a680866ff7e6c669f6",
                         "installed_by": ["modules"]
                     },
                     "genmod/score": {
                         "branch": "master",
-                        "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c",
+                        "git_sha": "f888300c726e1f817a9f93a680866ff7e6c669f6",
                         "installed_by": ["modules"]
                     },
                     "gfastats": {
diff --git a/modules/local/create_pedigree_file/main.nf b/modules/local/create_pedigree_file/main.nf
index 10ab7e81..fc6eca46 100644
--- a/modules/local/create_pedigree_file/main.nf
+++ b/modules/local/create_pedigree_file/main.nf
@@ -1,5 +1,5 @@
 process CREATE_PEDIGREE_FILE {
-    tag "${project}"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "conda-forge::python=3.8.3"
@@ -8,20 +8,20 @@ process CREATE_PEDIGREE_FILE {
         'biocontainers/python:3.8.3' }"
 
     input:
-    tuple val(project), val(meta)
+    tuple val(meta), val(metas)
 
     output:
-    tuple val(project), path("*.ped"), emit: ped
-    path "versions.yml"              , emit: versions
+    tuple val(meta), path("*.ped"), emit: ped
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def out   = new File(project + ".ped")
-    def samples = (meta.collect().size() > 1) ? meta.sort{ a, b ->
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    def samples = (metas.collect().size() > 1) ? metas.sort{ a, b ->
         // First sort on family_id, then on sample id
-        a.family_id <=> b.family_id ?: a.id <=> b.id } : meta
+        a.family_id <=> b.family_id ?: a.id <=> b.id } : metas
     outfile_text = ['#family_id', 'sample_id', 'father', 'mother', 'sex', 'phenotype'].join('\\t')
     def samples_list = []
     for(int i = 0; i<samples.size(); i++) {
@@ -32,7 +32,7 @@ process CREATE_PEDIGREE_FILE {
         }
     }
     """
-    echo -e "$outfile_text" >${project}.ped
+    echo -e "$outfile_text" > ${prefix}.ped
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -42,8 +42,9 @@ process CREATE_PEDIGREE_FILE {
     """
 
     stub:
+    def prefix   = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${project}.ped
+    touch ${prefix}.ped
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf
index ff71b660..a869221e 100644
--- a/modules/nf-core/genmod/models/main.nf
+++ b/modules/nf-core/genmod/models/main.nf
@@ -8,8 +8,7 @@ process GENMOD_MODELS {
         'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input_vcf)
-    path (fam)
+    tuple val(meta), path(input_vcf), path (fam)
     path (reduced_penetrance)
 
     output:
diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml
index dca74095..a6249114 100644
--- a/modules/nf-core/genmod/models/meta.yml
+++ b/modules/nf-core/genmod/models/meta.yml
@@ -22,9 +22,9 @@ input:
         type: file
         description: vcf file
         pattern: "*.{vcf}"
-  - - fam:
+    - fam:
         type: file
-        description: file with family information
+        description: PED file with family information
   - - reduced_penetrance:
         type: file
         description: file with gene ids that have reduced penetrance
diff --git a/modules/nf-core/genmod/models/tests/main.nf.test b/modules/nf-core/genmod/models/tests/main.nf.test
index afa85dfc..0b9a3ebd 100644
--- a/modules/nf-core/genmod/models/tests/main.nf.test
+++ b/modules/nf-core/genmod/models/tests/main.nf.test
@@ -15,10 +15,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
                 ]
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
-                input[2] = []
+                input[1] = []
                 """
             }
         }
@@ -44,10 +44,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
                 ]
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
-                input[2] = []
+                input[1] = []
                 """
             }
         }
diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf
index 41d57bdc..756fc731 100644
--- a/modules/nf-core/genmod/score/main.nf
+++ b/modules/nf-core/genmod/score/main.nf
@@ -8,8 +8,7 @@ process GENMOD_SCORE {
         'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input_vcf)
-    path (fam)
+    tuple val(meta), path(input_vcf), path (fam)
     path (score_config)
 
     output:
diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml
index 32da6468..c5fe2e2a 100644
--- a/modules/nf-core/genmod/score/meta.yml
+++ b/modules/nf-core/genmod/score/meta.yml
@@ -22,9 +22,9 @@ input:
         type: file
         description: vcf file
         pattern: "*.{vcf}"
-  - - fam:
+    - fam:
         type: file
-        description: file with family information
+        description: PED file with family information
   - - score_config:
         type: file
         description: rank model config file
diff --git a/modules/nf-core/genmod/score/tests/main.nf.test b/modules/nf-core/genmod/score/tests/main.nf.test
index 98c8f35a..6181f63a 100644
--- a/modules/nf-core/genmod/score/tests/main.nf.test
+++ b/modules/nf-core/genmod/score/tests/main.nf.test
@@ -15,10 +15,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
                 ]
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
-                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini', checkIfExists: true)
                 """
             }
         }
@@ -44,10 +44,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
                 ]
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
-                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini', checkIfExists: true)
                 """
             }
         }
diff --git a/subworkflows/local/rank_variants/main.nf b/subworkflows/local/rank_variants/main.nf
index c416b248..db7e0139 100644
--- a/subworkflows/local/rank_variants/main.nf
+++ b/subworkflows/local/rank_variants/main.nf
@@ -12,7 +12,7 @@ workflow RANK_VARIANTS {
 
     take:
     ch_vcf                // channel: [mandatory] [ val(meta), path(vcf) ]
-    ch_pedfile            // channel: [mandatory] [ val(meta), path(ped) ]
+    ch_ped                // channel: [mandatory] [ val(meta), path(ped) ]
     ch_reduced_penetrance // channel: [mandatory] [ val(meta), path(pentrance) ]
     ch_score_config       // channel: [mandatory] [ val(meta), path(ini) ]
 
@@ -22,16 +22,22 @@ workflow RANK_VARIANTS {
     GENMOD_ANNOTATE ( ch_vcf )
     ch_versions = ch_versions.mix(GENMOD_ANNOTATE.out.versions)
 
+    GENMOD_ANNOTATE.out.vcf
+        .join( ch_ped, failOnMismatch: true )
+        .set { genmod_models_in }
+
     GENMOD_MODELS (
-        GENMOD_ANNOTATE.out.vcf,
-        ch_pedfile.map { meta, ped -> ped },
+        genmod_models_in,
         ch_reduced_penetrance.map { meta, file -> file }
     )
     ch_versions = ch_versions.mix(GENMOD_MODELS.out.versions)
 
+    GENMOD_MODELS.out.vcf
+        .join( ch_ped, failOnMismatch: true )
+        .set { genmod_score_in }
+
     GENMOD_SCORE (
-        GENMOD_MODELS.out.vcf,
-        ch_pedfile.map { meta, ped -> ped },
+        genmod_score_in,
         ch_score_config.map { meta, file -> file }
     )
     ch_versions = ch_versions.mix(GENMOD_SCORE.out.versions)
diff --git a/subworkflows/local/rank_variants/tests/main.nf.test b/subworkflows/local/rank_variants/tests/main.nf.test
index 473f16c8..a544a445 100644
--- a/subworkflows/local/rank_variants/tests/main.nf.test
+++ b/subworkflows/local/rank_variants/tests/main.nf.test
@@ -28,7 +28,7 @@ nextflow_workflow {
             process {
                 """
                 input[0] = [
-                    [ id: 'test', num_intervals:1 ],
+                    [ id: 'project', num_intervals:1 ],
                     file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = PREPARE_GENOME.out.fasta
@@ -46,7 +46,7 @@ nextflow_workflow {
                 input[0] = MINIMAP2_ALIGN.out.bam
                             .join(MINIMAP2_ALIGN.out.index)
                             .join(Channel.of([
-                                [ id: 'test', num_intervals:1 ],
+                                [ id: 'project', num_intervals:1 ],
                                 file(params.pipelines_testdata_base_path + 'reference/test_data.bed', checkIfExists: true)
                             ]))
                 input[1] = PREPARE_GENOME.out.fasta
@@ -95,9 +95,9 @@ nextflow_workflow {
             process {
                 """
                 input[0] = [
-                    'project',
+                    [id:'project'],
                     [
-                        [ id: 'test', project: 'project', maternal_id: '0', paternal_id: '0', family_id: 'family', sex: '2', phenotype: '2' ]
+                        [ id: 'project', project: 'project', maternal_id: '0', paternal_id: '0', family_id: 'family', sex: '2', phenotype: '2' ]
                     ]
                 ]
                 """
@@ -110,8 +110,8 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = ANNOTATE_CSQ_PLI.out.vcf
-                input[1] = CREATE_PEDIGREE_FILE.out.ped
+                input[0] = ANNOTATE_CSQ_PLI.out.vcf.map { meta, vcf -> [ [ id: 'test' ], vcf ] }
+                input[1] = CREATE_PEDIGREE_FILE.out.ped.map { meta, ped -> [ [ id: 'test' ], ped ] }
                 input[2] = Channel.of([
                     [ id: 'reduced_penetrance' ],
                     file(params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv', checkIfExists: true)
@@ -142,8 +142,8 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = ANNOTATE_CSQ_PLI.out.vcf
-                input[1] = CREATE_PEDIGREE_FILE.out.ped
+                input[0] = ANNOTATE_CSQ_PLI.out.vcf.map { meta, vcf -> [ [ id: 'test' ], vcf ] }
+                input[1] = CREATE_PEDIGREE_FILE.out.ped.map { meta, ped -> [ [ id: 'test' ], ped ] }
                 input[2] = Channel.of([
                     [ id: 'reduced_penetrance' ],
                     file(params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv', checkIfExists: true)
diff --git a/subworkflows/local/rank_variants/tests/main.nf.test.snap b/subworkflows/local/rank_variants/tests/main.nf.test.snap
index 19326d68..a955bed6 100644
--- a/subworkflows/local/rank_variants/tests/main.nf.test.snap
+++ b/subworkflows/local/rank_variants/tests/main.nf.test.snap
@@ -15,21 +15,17 @@
                 "0": [
                     [
                         {
-                            "id": "test_data.bed",
-                            "project": null,
-                            "contains_affected": false
+                            "id": "test"
                         },
-                        "test_data.bed_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test_data.bed",
-                            "project": null,
-                            "contains_affected": false
+                            "id": "test"
                         },
-                        "test_data.bed_sorted.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_sorted.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -42,21 +38,17 @@
                 "tbi": [
                     [
                         {
-                            "id": "test_data.bed",
-                            "project": null,
-                            "contains_affected": false
+                            "id": "test"
                         },
-                        "test_data.bed_sorted.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_sorted.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "vcf": [
                     [
                         {
-                            "id": "test_data.bed",
-                            "project": null,
-                            "contains_affected": false
+                            "id": "test"
                         },
-                        "test_data.bed_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
@@ -72,6 +64,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-01T13:03:00.102392544"
+        "timestamp": "2024-11-04T14:34:36.22073696"
     }
 }
\ No newline at end of file
diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
index 3fbdad9a..9e77b8bc 100644
--- a/tests/samplesheet.nf.test.snap
+++ b/tests/samplesheet.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "test profile": {
         "content": [
-            111,
+            112,
             {
                 "ADD_FOUND_IN_TAG": {
                     "bcftools": 1.2,
@@ -185,6 +185,10 @@
                     "create_pedigree_file": 1.0,
                     "python": "3.8.3"
                 },
+                "SOMALIER_PED_FAMILY": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
                 "SPLITUBAM": {
                     "splitubam": "0.1.1"
                 },
@@ -301,7 +305,10 @@
                 "paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz",
                 "paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz.tbi",
                 "pedigree",
-                "pedigree/test.ped",
+                "pedigree/family",
+                "pedigree/family/FAM.ped",
+                "pedigree/project",
+                "pedigree/project/test.ped",
                 "phased_variants",
                 "phased_variants/HG002_Revio",
                 "phased_variants/HG002_Revio/HG002_Revio_phased.vcf.gz",
@@ -423,6 +430,7 @@
                 "multiqc_fastqc.txt:md5,f0717ca13d848aa8f5eaa5d0dba92178",
                 "multiqc_general_stats.txt:md5,c82b773e9d5ab3251280f3f03f35193a",
                 "multiqc_whatshap_stats.txt:md5,c8c212ecc6fbf6803f8de87f2395363f",
+                "FAM.ped:md5,bd5cec27ba7337a85cf98e787131e2b5",
                 "test.ped:md5,bd5cec27ba7337a85cf98e787131e2b5",
                 "HG002_Revio_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
                 "HG002_Revio_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
@@ -536,6 +544,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-31T16:12:33.482377002"
+        "timestamp": "2024-11-05T13:41:06.05402932"
     }
 }
\ No newline at end of file
diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap
index cb232f89..8c4a97ed 100644
--- a/tests/samplesheet_multisample_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "samplesheet_multisample_bam | --phaser hiphase": {
         "content": [
-            156,
+            157,
             {
                 "ADD_FOUND_IN_TAG": {
                     "bcftools": 1.2,
@@ -182,6 +182,10 @@
                     "create_pedigree_file": 1.0,
                     "python": "3.8.3"
                 },
+                "SOMALIER_PED_FAMILY": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
                 "SPLITUBAM": {
                     "splitubam": "0.1.1"
                 },
@@ -333,7 +337,10 @@
                 "paraphase/HG002_Revio_B/HG002_Revio_B_paraphase_vcfs/HG002_Revio_B_hba.vcf.gz",
                 "paraphase/HG002_Revio_B/HG002_Revio_B_paraphase_vcfs/HG002_Revio_B_hba.vcf.gz.tbi",
                 "pedigree",
-                "pedigree/test.ped",
+                "pedigree/family",
+                "pedigree/family/FAM.ped",
+                "pedigree/project",
+                "pedigree/project/test.ped",
                 "phased_variants",
                 "phased_variants/HG002_Revio_A",
                 "phased_variants/HG002_Revio_A/HG002_Revio_A_phased.blocks.tsv",
@@ -530,6 +537,7 @@
                 "multiqc_fastqc.txt:md5,18ca1a3fb2afa8988dc5d604c049cd9c",
                 "multiqc_general_stats.txt:md5,4a2c114e57d5581b606012d1604d51fa",
                 "multiqc_whatshap_stats.txt:md5,96447de4e14a9b4a570c24513de64970",
+                "FAM.ped:md5,24d8694d580f782ed77d4d1b5c6f6fb4",
                 "test.ped:md5,24d8694d580f782ed77d4d1b5c6f6fb4",
                 "HG002_Revio_A_phased.blocks.tsv:md5,27ce044ba581da15ef838cbb343a64cf",
                 "HG002_Revio_A_phased.stats.tsv:md5,58ae1b01d01b922d022ad025a81f1026",
@@ -733,6 +741,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-31T16:14:41.962593731"
+        "timestamp": "2024-11-05T13:42:51.526893089"
     }
 }
\ No newline at end of file
diff --git a/tests/samplesheet_multisample_ont_bam.nf.test.snap b/tests/samplesheet_multisample_ont_bam.nf.test.snap
index f186dfa3..cf41a33c 100644
--- a/tests/samplesheet_multisample_ont_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_ont_bam.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "samplesheet_multisample_ont_bam | --preset ONT_R10 --phaser whatshap --parallel_alignments 1 --parallel_snv 1": {
         "content": [
-            103,
+            104,
             {
                 "ADD_FOUND_IN_TAG": {
                     "bcftools": 1.2,
@@ -143,6 +143,10 @@
                     "create_pedigree_file": 1.0,
                     "python": "3.8.3"
                 },
+                "SOMALIER_PED_FAMILY": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
                 "SPLIT_BED_CHUNKS": {
                     "split_bed_chunks": 1.0
                 },
@@ -247,7 +251,10 @@
                 "paraphase/HG002_ONT_B/HG002_ONT_B_paraphase_vcfs/HG002_ONT_B_hba.vcf.gz",
                 "paraphase/HG002_ONT_B/HG002_ONT_B_paraphase_vcfs/HG002_ONT_B_hba.vcf.gz.tbi",
                 "pedigree",
-                "pedigree/test.ped",
+                "pedigree/family",
+                "pedigree/family/FAM.ped",
+                "pedigree/project",
+                "pedigree/project/test.ped",
                 "phased_variants",
                 "phased_variants/HG002_ONT_A",
                 "phased_variants/HG002_ONT_A/HG002_ONT_A_phased.vcf.gz",
@@ -375,6 +382,7 @@
                 "multiqc_fastqc.txt:md5,5254c5d578af3a24182ccf3248183ac6",
                 "multiqc_general_stats.txt:md5,0722f1462d3502d5383eb86a484192c6",
                 "multiqc_whatshap_stats.txt:md5,5c4b972c8d52b3d997f117b39ba3ad5d",
+                "FAM.ped:md5,deb1ee6bd38d6e8f7cb92801d8a12f12",
                 "test.ped:md5,deb1ee6bd38d6e8f7cb92801d8a12f12",
                 "HG002_ONT_A_cramino_aligned_phased.arrow:md5,d2a5c81595fa34925ab8f03078487d81",
                 "HG002_ONT_B_cramino_aligned_phased.arrow:md5,61af72539e105cec79db7c9b78eb15a7",
@@ -477,6 +485,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-31T16:16:52.848104929"
+        "timestamp": "2024-11-05T13:44:39.150334649"
     }
 }
\ No newline at end of file
diff --git a/workflows/nallo.nf b/workflows/nallo.nf
index 312ae3e0..84aee66d 100644
--- a/workflows/nallo.nf
+++ b/workflows/nallo.nf
@@ -40,6 +40,7 @@ include { SNV_ANNOTATION                          } from '../subworkflows/local/
 // local
 include { CREATE_PEDIGREE_FILE as SAMPLESHEET_PED           } from '../modules/local/create_pedigree_file/main'
 include { CREATE_PEDIGREE_FILE as SOMALIER_PED              } from '../modules/local/create_pedigree_file/main'
+include { CREATE_PEDIGREE_FILE as SOMALIER_PED_FAMILY       } from '../modules/local/create_pedigree_file/main'
 include { ECHTVAR_ENCODE                                    } from '../modules/local/echtvar/encode/main'
 include { SAMTOOLS_MERGE                                    } from '../modules/nf-core/samtools/merge/main'
 
@@ -190,7 +191,7 @@ workflow NALLO {
         // Create PED from samplesheet
         //
         ch_input
-            .map { meta, files -> [ meta.project, meta ] }
+            .map { meta, files -> [ [ id: meta.project ], meta ] }
             .groupTuple()
             .set { ch_samplesheet_ped_in }
 
@@ -198,7 +199,6 @@ workflow NALLO {
         ch_versions = ch_versions.mix(SAMPLESHEET_PED.out.versions)
 
         SAMPLESHEET_PED.out.ped
-            .map { project, ped -> [ [ 'id': project ], ped ] }
             .collect()
             .set { ch_samplesheet_pedfile }
 
@@ -216,10 +216,10 @@ workflow NALLO {
         bam_bai = BAM_INFER_SEX.out.bam_bai
 
         //
-        // Create PED with updated sex
+        // Create PED with updated sex per project (should perphaps be per SNV-calling region)
         //
         bam
-            .map { meta, files -> [ meta.project, meta ] }
+            .map { meta, files -> [ [ id: meta.project ], meta ] }
             .groupTuple()
             .set { ch_somalier_ped_in }
 
@@ -227,10 +227,23 @@ workflow NALLO {
         ch_versions = ch_versions.mix(SOMALIER_PED.out.versions)
 
         SOMALIER_PED.out.ped
-            .map { project, ped -> [ [ 'id': project ], ped ] }
             .collect()
             .set { ch_updated_pedfile }
 
+        //
+        // Create PED with updated sex - per family
+        //
+        bam
+            .map { meta, files -> [ [ id: meta.family_id ], meta ] }
+            .groupTuple()
+            .set { ch_somalier_ped_family_in }
+
+        SOMALIER_PED_FAMILY ( ch_somalier_ped_family_in )
+        ch_versions = ch_versions.mix(SOMALIER_PED_FAMILY.out.versions)
+
+        SOMALIER_PED_FAMILY.out.ped
+            .set { ch_updated_pedfile_family }
+
         //
         // Run read QC with FastQC, mosdepth and cramino
         //
@@ -356,6 +369,12 @@ workflow NALLO {
                 )
                 ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions)
 
+                // Give pedfile meta from
+                ANN_CSQ_PLI_SNV.out.vcf
+                    .combine(ch_updated_pedfile.map { meta, ped -> ped } )
+                    .map { meta, vcf, ped -> [ meta, ped ] }
+                    .set { rank_snvs_ped_in }
+
                 //
                 // Ranks one multisample VCF per variant call region
                 // Can only run if samplesheet has affected samples
@@ -364,7 +383,7 @@ workflow NALLO {
                     // Only run if we have affected individuals
                     RANK_VARIANTS_SNV (
                         ANN_CSQ_PLI_SNV.out.vcf,
-                        ch_updated_pedfile,
+                        rank_snvs_ped_in,
                         ch_reduced_penetrance,
                         ch_score_config_snv
                     )
@@ -534,7 +553,7 @@ workflow NALLO {
             if (!params.skip_rank_variants) {
                 RANK_VARIANTS_SVS (
                     ANN_CSQ_PLI_SVS.out.vcf,
-                    ch_updated_pedfile,
+                    ch_updated_pedfile_family,
                     ch_reduced_penetrance,
                     ch_score_config_svs
                 )