diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2216d131..b9f3cbfa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,13 +18,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Removed`
 
+- [#238](https://github.com/genomic-medicine-sweden/nallo/pull/238) - Removed the `--extra_gvcfs` parameter
+
 ### `Fixed`
 
 ### Parameters
 
-| Old parameter | New parameter              |
-| ------------- | -------------------------- |
-|               | `--deepvariant_model_type` |
+| Old parameter   | New parameter              |
+| --------------- | -------------------------- |
+|                 | `--deepvariant_model_type` |
+| `--extra_gvcfs` |                            |
 
 ## v0.2.0 - [2024-06-26]
 
diff --git a/docs/usage.md b/docs/usage.md
index 82b1f4d0..043ac92d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -133,20 +133,6 @@ HG01123,/path/to/HG01123_sniffles.snf
 HG01124,/path/to/HG01124_sniffles.snf
 ```
 
-- For SNVs - prepare a samplesheet with gVCF files from DeepVariant to supply with `--extra_gvcfs`:
-
-> [!NOTE]
-> These has to have been generated with the same version of reference genome.
-
-`extra_gvcfs.csv`
-
-```
-sample,file
-HG01123,/path/to/HG01123.g.vcf.gz
-HG01124,/path/to/HG01124.g.vcf.gz
-HG01125,/path/to/HG01125.g.vcf.gz
-```
-
 - If running without `--skip_call_paralogs`, the reference genome needs to be hg38
 
 - If running without `--skip_mapping_wf`, a VCF of known polymorphic sites (e.g. [sites.hg38.vcg.gz](https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz)) needs to be supplied with `--somalier_sites`, from which sex will be inferred if possible.
@@ -263,7 +249,6 @@ Different processes may need extra input files
 | Parameter                          | Description                                                                                                                                                                                                                                                               | Type      | Default | Required | Hidden |
 | ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ |
 | `dipcall_par`                      | Provide a bed file of chrX PAR regions for dipcall                                                                                                                                                                                                                        | `string`  |         |          |        |
-| `extra_gvcfs`                      | Extra input files for GLNexus                                                                                                                                                                                                                                             | `string`  |         |          |        |
 | `extra_snfs`                       | Extra input files for Sniffles                                                                                                                                                                                                                                            | `string`  |         |          |        |
 | `tandem_repeats`                   | Tandem repeat BED-file for sniffles                                                                                                                                                                                                                                       | `string`  |         |          |        |
 | `trgt_repeats`                     | BED-file for repeats to be genotyped                                                                                                                                                                                                                                      | `string`  |         |          |        |
diff --git a/nextflow.config b/nextflow.config
index 70e8cdde..b3a66e92 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,7 +14,6 @@ params {
     bed                        = null
     dipcall_par                = null
     extra_snfs                 = null
-    extra_gvcfs                = null
     tandem_repeats             = null
     trgt_repeats               = null
     snp_db                     = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 999a7e4d..c0faba57 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -392,14 +392,6 @@
                     "format": "file-path",
                     "exists": true
                 },
-                "extra_gvcfs": {
-                    "type": "string",
-                    "description": "Extra input files for GLNexus",
-                    "pattern": "^\\S+\\.csv$",
-                    "format": "file-path",
-                    "schema": "assets/schema_gvcfs.json",
-                    "exists": true
-                },
                 "extra_snfs": {
                     "type": "string",
                     "description": "Extra input files for Sniffles",
diff --git a/subworkflows/local/short_variant_calling/main.nf b/subworkflows/local/short_variant_calling/main.nf
index 1bfe58cd..3bee882e 100644
--- a/subworkflows/local/short_variant_calling/main.nf
+++ b/subworkflows/local/short_variant_calling/main.nf
@@ -1,7 +1,5 @@
 include { DEEPVARIANT                               } from '../../../modules/nf-core/deepvariant'
 include { GLNEXUS                                   } from '../../../modules/nf-core/glnexus'
-include { BCFTOOLS_VIEW_REGIONS                     } from '../../../modules/local/bcftools/view_regions'
-include { TABIX_TABIX as TABIX_EXTRA_GVCFS          } from '../../../modules/nf-core/tabix/tabix/main'
 include { TABIX_TABIX as TABIX_DV                   } from '../../../modules/nf-core/tabix/tabix/main'
 include { TABIX_TABIX as TABIX_DV_VCF               } from '../../../modules/nf-core/tabix/tabix/main'
 include { TABIX_TABIX as TABIX_GLNEXUS              } from '../../../modules/nf-core/tabix/tabix/main'
@@ -14,7 +12,6 @@ workflow SHORT_VARIANT_CALLING {
 
     take:
     ch_bam_bai_bed // channel: [ val(meta), path(bam), path(bai), path(call_region_bed) ]
-    ch_extra_gvcfs // channel: [ val(meta), path(gvcfs) ]
     ch_fasta       // channel: [ val(meta), path(fasta) ]
     ch_fai         // channel: [ val(meta), path(fai) ]
     ch_bed         // channel: [ val(meta), path(input_bed) ]
@@ -33,17 +30,6 @@ workflow SHORT_VARIANT_CALLING {
     // Collect GVCFs
     ch_snp_calls_gvcf = ch_snp_calls_gvcf.mix(DEEPVARIANT.out.gvcf)
 
-    // Extra gVCFs
-    TABIX_EXTRA_GVCFS(ch_extra_gvcfs)
-
-    ch_extra_gvcfs
-        .join(TABIX_EXTRA_GVCFS.out.tbi)
-        .groupTuple()
-        .set{ ch_bcftools_view_regions_in }
-
-    // This cuts all regions in BED file from extra gVCFS, better than nothing
-    BCFTOOLS_VIEW_REGIONS( ch_bcftools_view_regions_in, ch_bed )
-
     // DV gVCFs
     TABIX_DV(ch_snp_calls_gvcf)
 
@@ -52,7 +38,6 @@ workflow SHORT_VARIANT_CALLING {
         .join(TABIX_DV.out.tbi.groupTuple())
         .set{ bcftools_concat_dv_in }
 
-
     // Concat into one gVCF per sample & sort
     BCFTOOLS_CONCAT_DV ( bcftools_concat_dv_in )
     ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_DV.out.versions)
@@ -79,7 +64,6 @@ workflow SHORT_VARIANT_CALLING {
 
     // Put DV and extra gvCFs together -> send to glnexus
     BCFTOOLS_SORT_DV.out.vcf
-        .concat(BCFTOOLS_VIEW_REGIONS.out.vcf)
         .map { meta, gvcf -> [ ['id':'multisample'], gvcf ]}
         .groupTuple()
         .set{ ch_glnexus_in }
@@ -91,8 +75,6 @@ workflow SHORT_VARIANT_CALLING {
     // Get versions
     ch_versions = ch_versions.mix(DEEPVARIANT.out.versions)
     ch_versions = ch_versions.mix(GLNEXUS.out.versions)
-    ch_versions = ch_versions.mix(BCFTOOLS_VIEW_REGIONS.out.versions)
-    ch_versions = ch_versions.mix(TABIX_EXTRA_GVCFS.out.versions)
     ch_versions = ch_versions.mix(TABIX_DV.out.versions)
     ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_DV.out.versions)
     ch_versions = ch_versions.mix(BCFTOOLS_SORT_DV.out.versions)
diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test b/subworkflows/local/short_variant_calling/tests/main.nf.test
index 771db68b..497bb74c 100644
--- a/subworkflows/local/short_variant_calling/tests/main.nf.test
+++ b/subworkflows/local/short_variant_calling/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_workflow {
     config "./nextflow.config"
     workflow "SHORT_VARIANT_CALLING"
 
-    test("1 sample - no bed, [], fasta, fai, []") {
+    test("1 sample - no bed, fasta, fai, []") {
 
         when {
             workflow {
@@ -16,16 +16,15 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
                 ]
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [[],[]]
+                input[3] = [[],[]]
                 """
             }
         }
@@ -39,7 +38,7 @@ nextflow_workflow {
 
     }
 
-    test("1 sample - 1 bed, [], fasta, fai, []") {
+    test("1 sample - 1 bed, fasta, fai, []") {
 
         when {
             workflow {
@@ -50,16 +49,15 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [[],[]]
+                input[3] = [[],[]]
                 """
             }
         }
@@ -74,7 +72,7 @@ nextflow_workflow {
 
     }
 
-    test("1 sample - 1 bed, [], fasta, fai, bed") {
+    test("1 sample - 1 bed, fasta, fai, bed") {
 
         when {
             workflow {
@@ -85,16 +83,15 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [
+                input[3] = [
                     [ id:'bed'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
@@ -112,7 +109,7 @@ nextflow_workflow {
 
     }
 
-    test("1 sample - 2 bed, [], fasta, fai, bed") {
+    test("1 sample - 2 bed, fasta, fai, bed") {
 
         when {
             workflow {
@@ -131,16 +128,15 @@ nextflow_workflow {
                         file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true)
                     ]
                 )
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [
+                input[3] = [
                     [ id:'bed'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
@@ -158,7 +154,7 @@ nextflow_workflow {
 
     }
 
-    test("2 samples - 2 bed, [], fasta, fai, bed") {
+    test("2 samples - 2 bed, fasta, fai, bed") {
 
         when {
             workflow {
@@ -189,16 +185,15 @@ nextflow_workflow {
                         file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true)
                     ]
                 )
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [
+                input[3] = [
                     [ id:'bed'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
@@ -216,7 +211,7 @@ nextflow_workflow {
 
     }
 
-    test("1 sample - no bed, [], fasta, fai, [] - stub") {
+    test("1 sample - no bed, fasta, fai, [] - stub") {
 
         options "-stub"
 
@@ -229,16 +224,15 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
                 ]
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [[],[]]
+                input[3] = [[],[]]
                 """
             }
         }
@@ -253,7 +247,7 @@ nextflow_workflow {
 
     }
 
-    test("1 sample - 1 bed, [], fasta, fai, [] - stub") {
+    test("1 sample - 1 bed, fasta, fai, [] - stub") {
 
         options "-stub"
 
@@ -266,16 +260,15 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [[],[]]
+                input[3] = [[],[]]
                 """
             }
         }
@@ -290,7 +283,7 @@ nextflow_workflow {
 
     }
 
-    test("1 sample - 1 bed, [], fasta, fai, bed - stub") {
+    test("1 sample - 1 bed, fasta, fai, bed - stub") {
 
         options "-stub"
 
@@ -303,16 +296,15 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [
+                input[3] = [
                     [ id:'bed'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
@@ -330,7 +322,7 @@ nextflow_workflow {
 
     }
 
-    test("1 sample - 2 bed, [], fasta, fai, bed - stub") {
+    test("1 sample - 2 bed, fasta, fai, bed - stub") {
 
         options "-stub"
 
@@ -351,16 +343,15 @@ nextflow_workflow {
                         file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true)
                     ]
                 )
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [
+                input[3] = [
                     [ id:'bed'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
@@ -378,7 +369,7 @@ nextflow_workflow {
 
     }
 
-    test("2 samples - 2 bed, [], fasta, fai, bed - stub") {
+    test("2 samples - 2 bed, fasta, fai, bed - stub") {
 
         options "-stub"
 
@@ -411,16 +402,15 @@ nextflow_workflow {
                         file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true)
                     ]
                 )
-                input[1] = Channel.empty()
-                input[2] = [
+                input[1] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[3] = [
+                input[2] = [
                     [ id:'genome'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[4] = [
+                input[3] = [
                     [ id:'bed'],
                     file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
index 65c71b94..d4f2085b 100644
--- a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
+++ b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "1 sample - 1 bed, [], fasta, fai, bed - stub": {
+    "1 sample - 1 bed, fasta, fai, bed": {
         "content": [
             {
                 "0": [
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
                     ]
                 ],
                 "1": [
@@ -16,18 +16,18 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
                     ]
                 ],
                 "2": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -37,7 +37,7 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
                     ]
                 ],
                 "snp_calls_vcf": [
@@ -46,18 +46,18 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -68,9 +68,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-28T09:08:56.289754473"
+        "timestamp": "2024-06-28T17:46:21.204025161"
     },
-    "1 sample - 1 bed, [], fasta, fai, [] - stub": {
+    "2 samples - 2 bed, fasta, fai, bed": {
         "content": [
             {
                 "0": [
@@ -79,7 +79,14 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                    ],
+                    [
+                        {
+                            "id": "test2",
+                            "single_end": false
+                        },
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,0ce965213b3c4fa10f5e855e0254cc0e"
                     ]
                 ],
                 "1": [
@@ -87,18 +94,33 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "multisample.bcf:md5,b64046133e7bb7c6c9bc5bacfc4592b3"
                     ]
                 ],
                 "2": [
+                    "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
+                    "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
+                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -108,7 +130,7 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "multisample.bcf:md5,b64046133e7bb7c6c9bc5bacfc4592b3"
                     ]
                 ],
                 "snp_calls_vcf": [
@@ -117,18 +139,40 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                    ],
+                    [
+                        {
+                            "id": "test2",
+                            "single_end": false
+                        },
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,0ce965213b3c4fa10f5e855e0254cc0e"
                     ]
                 ],
                 "versions": [
+                    "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
+                    "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
+                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -139,9 +183,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-28T09:08:43.398200049"
+        "timestamp": "2024-06-28T17:47:23.709677761"
     },
-    "1 sample - 1 bed, [], fasta, fai, bed": {
+    "1 sample - 1 bed, fasta, fai, []": {
         "content": [
             {
                 "0": [
@@ -210,9 +254,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-26T21:19:29.875734506"
+        "timestamp": "2024-06-28T17:45:52.755681185"
     },
-    "1 sample - no bed, [], fasta, fai, []": {
+    "1 sample - 2 bed, fasta, fai, bed - stub": {
         "content": [
             {
                 "0": [
@@ -221,7 +265,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -229,18 +273,21 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
+                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -250,7 +297,7 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
+                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "snp_calls_vcf": [
@@ -259,18 +306,21 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -281,9 +331,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-28T10:26:42.351783606"
+        "timestamp": "2024-06-28T17:48:17.863172363"
     },
-    "2 samples - 2 bed, [], fasta, fai, bed": {
+    "2 samples - 2 bed, fasta, fai, bed - stub": {
         "content": [
             {
                 "0": [
@@ -292,14 +342,14 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,0ce965213b3c4fa10f5e855e0254cc0e"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -307,7 +357,7 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,b64046133e7bb7c6c9bc5bacfc4592b3"
+                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -317,21 +367,21 @@
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
@@ -343,7 +393,7 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,b64046133e7bb7c6c9bc5bacfc4592b3"
+                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "snp_calls_vcf": [
@@ -352,14 +402,14 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,0ce965213b3c4fa10f5e855e0254cc0e"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
@@ -369,21 +419,21 @@
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
@@ -396,9 +446,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-26T21:21:54.809167844"
+        "timestamp": "2024-06-28T17:48:33.855199338"
     },
-    "1 sample - 1 bed, [], fasta, fai, []": {
+    "1 sample - no bed, fasta, fai, []": {
         "content": [
             {
                 "0": [
@@ -467,9 +517,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-26T21:18:55.954908032"
+        "timestamp": "2024-06-28T17:45:24.32759434"
     },
-    "1 sample - no bed, [], fasta, fai, [] - stub": {
+    "1 sample - 1 bed, fasta, fai, [] - stub": {
         "content": [
             {
                 "0": [
@@ -538,9 +588,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-28T10:28:58.425875863"
+        "timestamp": "2024-06-28T17:47:49.907226308"
     },
-    "1 sample - 2 bed, [], fasta, fai, bed": {
+    "1 sample - 1 bed, fasta, fai, bed - stub": {
         "content": [
             {
                 "0": [
@@ -549,7 +599,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -557,21 +607,18 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
+                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -581,7 +628,7 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
+                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "snp_calls_vcf": [
@@ -590,21 +637,18 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
+                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
+                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
-                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
-                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -615,9 +659,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-26T21:20:20.752118695"
+        "timestamp": "2024-06-28T17:48:03.133920517"
     },
-    "2 samples - 2 bed, [], fasta, fai, bed - stub": {
+    "1 sample - no bed, fasta, fai, [] - stub": {
         "content": [
             {
                 "0": [
@@ -627,13 +671,6 @@
                             "single_end": false
                         },
                         "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ],
-                    [
-                        {
-                            "id": "test2",
-                            "single_end": false
-                        },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -645,29 +682,14 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
                     "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
                     "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
-                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -687,39 +709,17 @@
                             "single_end": false
                         },
                         "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ],
-                    [
-                        {
-                            "id": "test2",
-                            "single_end": false
-                        },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
-                    "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
                     "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
                     "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
                     "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
-                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
-                    "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -730,9 +730,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-28T09:09:26.366065596"
+        "timestamp": "2024-06-28T17:47:36.537498338"
     },
-    "1 sample - 2 bed, [], fasta, fai, bed - stub": {
+    "1 sample - 2 bed, fasta, fai, bed": {
         "content": [
             {
                 "0": [
@@ -741,7 +741,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
                     ]
                 ],
                 "1": [
@@ -749,21 +749,21 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
                     ]
                 ],
                 "2": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -773,7 +773,7 @@
                         {
                             "id": "multisample"
                         },
-                        "multisample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "multisample.bcf:md5,51e2a9de1a43bfb041040ad04c61b4db"
                     ]
                 ],
                 "snp_calls_vcf": [
@@ -782,21 +782,21 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "concat_dv_vcf.vcf.gz_sorted.vcf.gz:md5,d8a35574801cfec345629770bfae2de7"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,38a1582fc609ee8377f3886a5ebca2d5",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
                     "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,7cb036286d153d15eea690e9a10a5ce4",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
-                    "versions.yml:md5,9745bff5dc75d55770369e32bc8f3ceb",
                     "versions.yml:md5,9fc1f49f5f53c7632a62df4cc241fe87",
-                    "versions.yml:md5,a892c0e39dcdd490a66509569ce4137c",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
+                    "versions.yml:md5,bde7cbe90248255755f0b32582174a9e",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
                     "versions.yml:md5,bf43ab2e9ad507743150a308745a1eff",
+                    "versions.yml:md5,c21eaade044c570ce3384fb22ba4c5fb",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
+                    "versions.yml:md5,c69d0d4be6b316a859ac77cf0f38e0b0",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,da8068d97833cacf511ffe498131adaa",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
@@ -807,6 +807,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-28T09:09:10.021442882"
+        "timestamp": "2024-06-28T17:46:50.879572276"
     }
 }
\ No newline at end of file
diff --git a/workflows/nallo.nf b/workflows/nallo.nf
index 914ed0e7..f572e3c1 100644
--- a/workflows/nallo.nf
+++ b/workflows/nallo.nf
@@ -65,8 +65,6 @@ workflow NALLO {
                                                 : ''
     ch_extra_snfs      = params.extra_snfs      ? Channel.fromSamplesheet('extra_snfs')
                                                 : Channel.empty()
-    ch_extra_gvcfs     = params.extra_gvcfs     ? Channel.fromSamplesheet('extra_gvcfs')
-                                                : Channel.empty()
     ch_tandem_repeats  = params.tandem_repeats  ? Channel.fromPath(params.tandem_repeats).map{ [ it.getSimpleName(), it]}.collect()
                                                 : Channel.value([[],[]])
     ch_bed             = params.bed             ? Channel.fromPath(params.bed).map{ [ it.getSimpleName(), it]}.collect()
@@ -268,7 +266,7 @@ workflow NALLO {
 
         if(!params.skip_short_variant_calling) {
             // Call SNVs with DeepVariant/DeepTrio
-            SHORT_VARIANT_CALLING( ch_snv_calling_in , ch_extra_gvcfs, fasta, fai, ch_bed )
+            SHORT_VARIANT_CALLING( ch_snv_calling_in, fasta, fai, ch_bed )
             ch_versions = ch_versions.mix(SHORT_VARIANT_CALLING.out.versions)
 
             if(!params.skip_snv_annotation) {