diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4b51ffb2e..4579b97cd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#962](https://github.com/genomic-medicine-sweden/nallo/pull/962) - Changed peddy inputs from ranked to annotated or unannotated variants, depending on availability
 - [#964](https://github.com/genomic-medicine-sweden/nallo/pull/964) - Limit `--snv_calling_processes` to `1` for sentieon due to issues with duplicated variants (see #926)
 - [#966](https://github.com/genomic-medicine-sweden/nallo/pull/966) - Refactored the code related to variant ranking to reduce code duplication
+- [#969](https://github.com/genomic-medicine-sweden/nallo/pull/969) - Split hifiasm process into two so they can have different resources: first only create bins then assembly with the bins already created
 - [#974](https://github.com/genomic-medicine-sweden/nallo/pull/974) - Updated FastQC nf-core module
 - [#975](https://github.com/genomic-medicine-sweden/nallo/pull/975) - Moved params from `nallo.nf` to main workflow
 - [#975](https://github.com/genomic-medicine-sweden/nallo/pull/975) - Renamed `ch_databases` to `ch_echtvar_databases` for clarity
diff --git a/conf/base.config b/conf/base.config
index 757b07642..5adf7ff9d 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -50,7 +50,7 @@ process {
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
-    withName: 'HIFIASM' {
+    withName: 'HIFIASM_ASSEMBLY|HIFIASM_BINS' {
         time   = { 36.h  * task.attempt }
     }
     withLabel:error_ignore {
diff --git a/conf/modules/genome_assembly.config b/conf/modules/genome_assembly.config
index 98a0dc3f2..822586721 100644
--- a/conf/modules/genome_assembly.config
+++ b/conf/modules/genome_assembly.config
@@ -24,12 +24,13 @@ process {
         ]
     }
 
-    withName: '.*:GENOME_ASSEMBLY:HIFIASM' {
+    withName: '.*:GENOME_ASSEMBLY:HIFIASM_ASSEMBLY|.*:GENOME_ASSEMBLY:HIFIASM_BINS' {
         ext.args = { [
             "${params.extra_hifiasm_options}",
             "${params.hifiasm_preset}",
             '--dual-scaf',
-            '--telo-m CCCTAA'
+            '--telo-m CCCTAA',
+            '--bin-only'
         ].join(' ') }
     }
 
diff --git a/modules.json b/modules.json
index ab62bfc85..6eda2a976 100644
--- a/modules.json
+++ b/modules.json
@@ -203,7 +203,7 @@
                     },
                     "hifiasm": {
                         "branch": "master",
-                        "git_sha": "b00cfb8947da7842e8f249cc0c5bb8544cfac18e",
+                        "git_sha": "a20dba808c5ce99afe6d40d7fc072c74ca317c8d",
                         "installed_by": ["modules"]
                     },
                     "hificnv": {
diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf
index dce2c467a..585227b9e 100644
--- a/modules/nf-core/hifiasm/main.nf
+++ b/modules/nf-core/hifiasm/main.nf
@@ -9,12 +9,12 @@ process HIFIASM {
 
     input:
     tuple val(meta) , path(long_reads)        , path(ul_reads)
-    tuple val(meta1), path(paternal_kmer_dump), path(maternal_kmer_dump)
-    tuple val(meta2), path(hic_read1)         , path(hic_read2)
-    tuple val(meta3), path(bin_files)
+    tuple val(meta2), path(paternal_kmer_dump), path(maternal_kmer_dump)
+    tuple val(meta3), path(hic_read1)         , path(hic_read2)
+    tuple val(meta4), path(bin_files)
 
     output:
-    tuple val(meta), path("*.r_utg.gfa")                             , emit: raw_unitigs
+    tuple val(meta), path("*.r_utg.gfa")                             , emit: raw_unitigs      , optional: true
     tuple val(meta), path("*.bin")                                   , emit: bin_files        , optional: true
     tuple val(meta), path("*.p_utg.gfa")                             , emit: processed_unitigs, optional: true
     tuple val(meta), path("${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa"), emit: primary_contigs  , optional: true
diff --git a/modules/nf-core/hifiasm/meta.yml b/modules/nf-core/hifiasm/meta.yml
index 9c32bb274..44cf76c9d 100644
--- a/modules/nf-core/hifiasm/meta.yml
+++ b/modules/nf-core/hifiasm/meta.yml
@@ -32,7 +32,7 @@ input:
         type: file
         description: ONT long reads to use with --ul.
         ontologies: []
-  - - meta1:
+  - - meta2:
         type: map
         description: |
           Groovy Map containing information about parental kmers.
@@ -46,7 +46,7 @@ input:
         description: Yak kmer dump file for maternal reads (can be used for
           haplotype resolution). It can have an arbitrary extension.
         ontologies: []
-  - - meta2:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing information about Hi-C reads
@@ -58,7 +58,7 @@ input:
         type: file
         description: Hi-C data Reverse reads.
         ontologies: []
-  - - meta3:
+  - - meta4:
         type: map
         description: |
           Groovy Map containing information about the input bin files
diff --git a/modules/nf-core/hifiasm/tests/main.nf.test b/modules/nf-core/hifiasm/tests/main.nf.test
index d158847b3..a8207d2af 100644
--- a/modules/nf-core/hifiasm/tests/main.nf.test
+++ b/modules/nf-core/hifiasm/tests/main.nf.test
@@ -12,7 +12,7 @@ nextflow_process {
     test("homo_sapiens pacbio hifi [fastq, [,], [,], [,]]") {
         when {
             params {
-                extra_output = "--write-ec --write-paf"
+                module_args = "-f0 --write-ec --write-paf"
             }
 
             process {
@@ -98,7 +98,8 @@ nextflow_process {
 
         when {
             params {
-                extra_output = ""
+                setup_args = '-f0 --bin-only'
+                module_args = '-f0'
             }
 
             process {
@@ -143,7 +144,7 @@ nextflow_process {
 
         when {
             params {
-                extra_output = ""
+                module_args = "-f0"
             }
 
             process {
@@ -200,7 +201,7 @@ nextflow_process {
     test("homo_sapiens pacbio hifi [fastq, [yak, yak], [,], [,] ]") {
         when {
             params {
-                extra_output = ""
+                module_args = "-f0"
             }
 
             process {
@@ -258,7 +259,7 @@ nextflow_process {
     test("homo_sapiens pacbio hifi [fastq, [,], [fastq, fastq], [,] ]") {
         when {
             params {
-                extra_output = ""
+                module_args = "-f0"
             }
 
             process {
@@ -318,7 +319,7 @@ nextflow_process {
     test("homo_sapiens pacbio hifi [fastq, [yak, yak], [fastq, fastq], [,] ]") {
         when {
             params {
-                extra_output = ""
+                module_args = "-f0"
             }
             process {
                 """
@@ -354,7 +355,7 @@ nextflow_process {
     test("homo_sapiens pacbio hifi [fastq, [yak, ], [,], [,] ]") {
         when {
             params {
-                extra_output = ""
+                module_args = "-f0"
             }
 
             process {
@@ -387,7 +388,7 @@ nextflow_process {
     test("homo_sapiens pacbio hifi [fastq, [,], [, fastq], [,] ]") {
         when {
             params {
-                extra_output = ""
+                module_args = "-f0"
             }
 
             process {
@@ -421,7 +422,7 @@ nextflow_process {
         options "-stub"
         when {
             params {
-                extra_output = ""
+                module_args = "-f0"
             }
 
             process {
diff --git a/modules/nf-core/hifiasm/tests/nextflow.config b/modules/nf-core/hifiasm/tests/nextflow.config
index ead4b539a..833326b45 100644
--- a/modules/nf-core/hifiasm/tests/nextflow.config
+++ b/modules/nf-core/hifiasm/tests/nextflow.config
@@ -1,3 +1,8 @@
 process {
-    ext.args = "-f0 ${params.extra_output}"
+    withName: "HIFIASM" {
+        ext.args = params.module_args
+    }
+    withName: "HIFIASM_INITIAL" {
+        ext.args = { params.setup_args ?: '' }
+    }
 }
diff --git a/subworkflows/local/genome_assembly/main.nf b/subworkflows/local/genome_assembly/main.nf
index 963f019f0..4fb412ccf 100644
--- a/subworkflows/local/genome_assembly/main.nf
+++ b/subworkflows/local/genome_assembly/main.nf
@@ -1,15 +1,15 @@
-include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main'
-include { HIFIASM   } from '../../../modules/nf-core/hifiasm'
-include { YAK_COUNT } from '../../../modules/nf-core/yak/count/main'
-include { GFASTATS  } from '../../../modules/nf-core/gfastats/main'
+include { CAT_FASTQ                   } from '../../../modules/nf-core/cat/fastq/main'
+include { HIFIASM as HIFIASM_BINS     } from '../../../modules/nf-core/hifiasm'
+include { HIFIASM as HIFIASM_ASSEMBLY } from '../../../modules/nf-core/hifiasm'
+include { YAK_COUNT                   } from '../../../modules/nf-core/yak/count/main'
+include { GFASTATS                    } from '../../../modules/nf-core/gfastats/main'
 
 // This subworkflow assembles and outputs haplotypes from a set of reads (grouped per sample), using hifiasm and gfastats.
 // It assumes that while each sample can have multiple files, each sample belongs to one family at most.
 workflow GENOME_ASSEMBLY {
-
     take:
-    ch_reads     // channel: [ val(meta), fastqs ]
-    trio_binning //    bool: Should we use trio binning mode where possible?
+    ch_reads // channel: [ val(meta), fastqs ]
+    trio_binning // bool: Should we use trio binning mode where possible?
 
     main:
     if (trio_binning) {
@@ -17,9 +17,9 @@ workflow GENOME_ASSEMBLY {
         ch_reads
             .branch { meta, _reads ->
                 def is_parent = meta.relationship in ['father', 'mother']
-                paired_parents             : is_parent && meta.has_other_parent
-                children_with_both_parents : meta.relationship == 'child' && meta.two_parents
-                other                      : true
+                paired_parents: is_parent && meta.has_other_parent
+                children_with_both_parents: meta.relationship == 'child' && meta.two_parents
+                other: true
             }
             .set { ch_branched_samples }
 
@@ -32,17 +32,15 @@ workflow GENOME_ASSEMBLY {
             }
             .set { ch_paired_parents_for_yak }
 
-        CAT_FASTQ (
+        CAT_FASTQ(
             ch_paired_parents_for_yak.cat
         )
 
-        YAK_COUNT (
+        YAK_COUNT(
             CAT_FASTQ.out.reads.concat(ch_paired_parents_for_yak.no_cat)
         )
 
         YAK_COUNT.out.yak
-            // Because a parent can have multiple children, and meta.children is a list of all children,
-            // we need to return one tuple per child.
             .flatMap { meta, yak ->
                 (meta.children ?: []).collect { child_id ->
                     [child_id, meta, yak]
@@ -50,19 +48,19 @@ workflow GENOME_ASSEMBLY {
             }
             .branch { child_id, meta, yak ->
                 paternal: meta.relationship == 'father'
-                    return [ child_id, yak ]
+                return [child_id, yak]
                 maternal: meta.relationship == 'mother'
-                    return [ child_id, yak ]
+                return [child_id, yak]
             }
             .set { ch_yak_output }
 
         // Creates the input for trio-binned assemblies (children with both parents)
         ch_branched_samples.children_with_both_parents
-            .map { meta, reads -> [ meta.id, meta, reads ] }
+            .map { meta, reads -> [meta.id, meta, reads] }
             .join(ch_yak_output.paternal)
             .join(ch_yak_output.maternal)
             .map { _id, meta, reads, yak_paternal, yak_maternal ->
-                [ meta, reads, yak_paternal, yak_maternal ]
+                [meta, reads, yak_paternal, yak_maternal]
             }
             .set { ch_with_both_parents }
 
@@ -70,36 +68,55 @@ workflow GENOME_ASSEMBLY {
         ch_branched_samples.other
             .concat(ch_branched_samples.paired_parents)
             .map { meta, fastqs ->
-                [ meta, fastqs, [], [] ]
+                [meta, fastqs, [], []]
             }
             .concat(ch_with_both_parents)
             .multiMap { meta, reads, yak_paternal, yak_maternal ->
-                reads : [ meta, reads       , []           ]
-                yak   : [ meta, yak_paternal, yak_maternal ]
+                reads: [meta, reads, []]
+                yak: [meta, yak_paternal, yak_maternal]
             }
             .set { ch_hifiasm_in }
-    } else {
+    }
+    else {
         ch_reads
             .multiMap { meta, reads ->
-                reads : [ meta, reads, [] ]
-                yak   : [ [], [], [] ]
+                reads: [meta, reads, []]
+                yak: [meta, [], []]
             }
             .set { ch_hifiasm_in }
     }
 
-    HIFIASM (
+    HIFIASM_BINS(
         ch_hifiasm_in.reads,
         ch_hifiasm_in.yak,
-        [[],[],[]],
-        [[],[]]
+        [[], [], []],
+        [[], []],
+    )
+
+    // Explicitly key bins/reads/yak by sample ID before assembly so each sample gets its own bins and yaks.
+    ch_hifiasm_in.reads
+        .join(ch_hifiasm_in.yak, failOnMismatch: true, failOnDuplicate: true)
+        .join(HIFIASM_BINS.out.bin_files, failOnMismatch: true, failOnDuplicate: true)
+        .multiMap { meta, reads, ul_reads, yak_paternal, yak_maternal, bin_files ->
+            reads: [meta, reads, ul_reads]
+            bins: [meta, bin_files]
+            yak: [meta, yak_paternal, yak_maternal]
+        }
+        .set { ch_hifiasm_assembly_in }
+
+    HIFIASM_ASSEMBLY(
+        ch_hifiasm_assembly_in.reads,
+        ch_hifiasm_assembly_in.yak,
+        [[], [], []],
+        ch_hifiasm_assembly_in.bins,
     )
 
-    HIFIASM.out.hap1_contigs
-        .map { meta, fasta -> [ meta + [ 'haplotype': 1 ], fasta ] }
+    HIFIASM_ASSEMBLY.out.hap1_contigs
+        .map { meta, fasta -> [meta + ['haplotype': 1], fasta] }
         .set { ch_gfastats_paternal_in }
 
-    HIFIASM.out.hap2_contigs
-        .map { meta, fasta -> [ meta + [ 'haplotype': 2 ], fasta ] }
+    HIFIASM_ASSEMBLY.out.hap2_contigs
+        .map { meta, fasta -> [meta + ['haplotype': 2], fasta] }
         .set { ch_gfastats_maternal_in }
 
     GFASTATS(
@@ -107,10 +124,10 @@ workflow GENOME_ASSEMBLY {
         'fasta',
         '',
         '',
-        [[],[]],
-        [[],[]],
-        [[],[]],
-        [[],[]]
+        [[], []],
+        [[], []],
+        [[], []],
+        [[], []],
     )
 
     emit:
diff --git a/subworkflows/local/genome_assembly/tests/main.nf.test b/subworkflows/local/genome_assembly/tests/main.nf.test
index 09844f1d5..2ce21e6ae 100644
--- a/subworkflows/local/genome_assembly/tests/main.nf.test
+++ b/subworkflows/local/genome_assembly/tests/main.nf.test
@@ -20,11 +20,10 @@ nextflow_workflow {
             }
         }
         then {
-
             assertAll(
                 { assert workflow.success },
                 { assert workflow.out.assembled_haplotypes.size() == 2 },
-                { assert workflow.trace.succeeded().size() == 3 }, // 3 tasks: 1x HIFIASM 2x GFASTATS
+                { assert workflow.trace.succeeded().size() == 4 }, // 4 tasks: 1x HIFIASM_BINS, 1x HIFIASM_ASSEMBLY, 2x GFASTATS
                 { assert snapshot(workflow.out).match() }
             )
         }
@@ -71,7 +70,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.trace.succeeded().size() == 14 }, // 14 tasks: 3x FASTQ, 2x YAK_COUNT, 3x HIFIASM 6x GFASTATS.
+                { assert workflow.trace.succeeded().size() == 17 }, // 17 tasks: 3x FASTQ, 2x YAK_COUNT, 3x HIFIASM_ASSEMBLY, 3x HIFIASM_BINS, 6x GFASTATS.
                 { assert workflow.out.assembled_haplotypes.size() == 6 },
                 { assert snapshot(workflow.out).match() }
             )
@@ -125,7 +124,7 @@ nextflow_workflow {
                 // other than a manual .view() on `ch_with_both_parents`, without adding the
                 // `ch_with_both_parents` intermediate channel to the output.
                 { assert workflow.success },
-                { assert workflow.trace.succeeded().size() == 18 }, // 14 tasks: 4x FASTQ, 2x YAK_COUNT, 4x HIFIASM 8x GFASTATS.
+                { assert workflow.trace.succeeded().size() == 22 }, // 22 tasks: 4x FASTQ, 2x YAK_COUNT, 4x HIFIASM_BINS, 4x HIFIASM_ASSEMBLY, 8x GFASTATS.
                 { assert workflow.out.assembled_haplotypes.size() == 8 },
                 { assert snapshot(workflow.out).match() }
             )
@@ -170,7 +169,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.trace.succeeded().size() == 8 }, // 8 tasks: 2x FASTQ, 2x HIFIASM 4x GFASTATS.
+                { assert workflow.trace.succeeded().size() == 10 }, // 10 tasks: 2x FASTQ, 2x HIFIASM_BINS, 2x HIFIASM_ASSEMBLY, 4x GFASTATS.
                 { assert workflow.out.assembled_haplotypes.size() == 4 },
                 { assert snapshot(workflow.out).match() }
             )
@@ -198,7 +197,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert workflow.out.assembled_haplotypes.size() == 2 },
-                { assert workflow.trace.succeeded().size() == 3 }, // 3 tasks: 1x HIFIASM 2x GFASTATS
+                { assert workflow.trace.succeeded().size() == 4 }, // 4 tasks: 1x HIFIASM_BINS, 1x HIFIASM_ASSEMBLY, 2x GFASTATS
                 { assert snapshot(workflow.out).match() }
             )
         }
@@ -229,7 +228,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert workflow.out.assembled_haplotypes.size() == 2 },
-                { assert workflow.trace.succeeded().size() == 3 }, // 3 tasks: 1x HIFIASM 2x GFASTATS
+                { assert workflow.trace.succeeded().size() == 4 }, // 4 tasks: 1x HIFIASM_BINS, 1x HIFIASM_ASSEMBLY, 2x GFASTATS
                 { assert snapshot(workflow.out).match() }
             )
         }
@@ -278,7 +277,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.trace.succeeded().size() == 14 }, // 14 tasks: 3x FASTQ, 2x YAK_COUNT, 3x HIFIASM 6x GFASTATS.
+                { assert workflow.trace.succeeded().size() == 17 }, // 17 tasks: 3x FASTQ, 2x YAK_COUNT, 3x HIFIASM_BINS, 3x HIFIASM_ASSEMBLY, 6x GFASTATS.
                 { assert workflow.out.assembled_haplotypes.size() == 6 },
                 { assert snapshot(workflow.out).match() }
             )
diff --git a/subworkflows/local/genome_assembly/tests/main.nf.test.snap b/subworkflows/local/genome_assembly/tests/main.nf.test.snap
index 1f9c15ff3..04caa42fb 100644
--- a/subworkflows/local/genome_assembly/tests/main.nf.test.snap
+++ b/subworkflows/local/genome_assembly/tests/main.nf.test.snap
@@ -44,11 +44,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T16:58:10.652835085",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-27T16:58:10.652835085"
+        }
     },
     "two children with two parents, trio-binning mode": {
         "content": [
@@ -291,11 +291,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-04-22T12:07:24.83452037",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-27T16:57:45.252123092"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.2"
+        }
     },
     "child with one parent, trio-binning mode -stub": {
         "content": [
@@ -418,11 +418,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T16:57:54.591328042",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-27T16:57:54.591328042"
+        }
     },
     "child with two parents, trio-binning mode": {
         "content": [
@@ -601,11 +601,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-04-22T12:03:31.707774681",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-27T16:57:11.460996721"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.2"
+        }
     },
     "one sample, hifi-only mode -stub": {
         "content": [
@@ -652,11 +652,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T16:58:02.560119499",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-27T16:58:02.560119499"
+        }
     },
     "one sample, hifi-only mode": {
         "content": [
@@ -703,11 +703,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T16:56:43.261998747",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-27T16:56:43.261998747"
+        }
     },
     "child with two parents, trio-binning mode -stub": {
         "content": [
@@ -886,10 +886,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T16:58:20.771161421",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-27T16:58:20.771161421"
+        }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/genome_assembly/tests/nextflow.config b/subworkflows/local/genome_assembly/tests/nextflow.config
index bb725f8cf..1af118c4f 100644
--- a/subworkflows/local/genome_assembly/tests/nextflow.config
+++ b/subworkflows/local/genome_assembly/tests/nextflow.config
@@ -1,9 +1,10 @@
 process {
-    withName: 'HIFIASM' {
+    withName: 'HIFIASM_ASSEMBLY|HIFIASM_BINS' {
         ext.args = { [
             '--dual-scaf',
             '--telo-m CCCTAA',
-            '-f0 -k30 -w30 -D10 -r1 -N1'
+            '-f0 -k30 -w30 -D10 -r1 -N1',
+            '--bin-only'
         ].join(' ') }
     }
 
diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
index 7ee09ea8a..7709cf576 100644
--- a/tests/samplesheet.nf.test.snap
+++ b/tests/samplesheet.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "test profile": {
         "content": [
-            226,
+            227,
             {
                 "BCFTOOLS_CONCAT": {
                     "bcftools": 1.21
@@ -134,7 +134,10 @@
                 "GUNZIP_FASTA": {
                     "gunzip": 1.13
                 },
-                "HIFIASM": {
+                "HIFIASM_ASSEMBLY": {
+                    "hifiasm": "0.25.0-r726"
+                },
+                "HIFIASM_BINS": {
                     "hifiasm": "0.25.0-r726"
                 },
                 "HIFICNV": {
@@ -828,10 +831,10 @@
                 
             ]
         ],
-        "timestamp": "2026-04-02T14:06:17.614655049",
+        "timestamp": "2026-04-08T15:06:21.502601043",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     }
 }
\ 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 3bb72549e..e53c00df5 100644
--- a/tests/samplesheet_multisample_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "samplesheet_multisample_bam": {
         "content": [
-            391,
+            394,
             {
                 "BCFTOOLS_CONCAT": {
                     "bcftools": 1.21
@@ -134,7 +134,10 @@
                 "GUNZIP_FASTA": {
                     "gunzip": 1.13
                 },
-                "HIFIASM": {
+                "HIFIASM_ASSEMBLY": {
+                    "hifiasm": "0.25.0-r726"
+                },
+                "HIFIASM_BINS": {
                     "hifiasm": "0.25.0-r726"
                 },
                 "HIFICNV": {
@@ -1304,10 +1307,10 @@
                 
             ]
         ],
-        "timestamp": "2026-04-02T14:06:46.903278137",
+        "timestamp": "2026-04-08T15:10:24.155468815",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     }
 }
\ 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 5df1400ab..1b702ba34 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 --alignment_processes 1 --snv_calling_processes 1 --sv_caller sniffles --publish_unannotated_family_svs": {
         "content": [
-            346,
+            349,
             {
                 "BCFTOOLS_CONCAT": {
                     "bcftools": 1.21
@@ -121,7 +121,10 @@
                 "GUNZIP_FASTA": {
                     "gunzip": 1.13
                 },
-                "HIFIASM": {
+                "HIFIASM_ASSEMBLY": {
+                    "hifiasm": "0.25.0-r726"
+                },
+                "HIFIASM_BINS": {
                     "hifiasm": "0.25.0-r726"
                 },
                 "HIFICNV": {
@@ -1229,10 +1232,10 @@
                 
             ]
         ],
-        "timestamp": "2026-04-02T14:06:48.82914627",
+        "timestamp": "2026-04-08T15:14:16.98293374",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/samplesheet_stub.nf.test b/tests/samplesheet_stub.nf.test
index b68a882c3..a01d0e28b 100644
--- a/tests/samplesheet_stub.nf.test
+++ b/tests/samplesheet_stub.nf.test
@@ -132,7 +132,7 @@ nextflow_pipeline {
             def versions = removeNextflowVersion("$outputDir/pipeline_info/nallo_software_mqc_versions.yml")
             assertAll(
                 { assert workflow.success },
-                { assert !versions.containsKey('HIFIASM') },
+                { assert !versions.containsKey('HIFIASM_ASSEMBLY') },
                 { assert versions.containsKey('SPLITUBAM') },
                 { assert stable_name.contains('aligned_reads') },
                 { assert snapshot(
@@ -178,7 +178,7 @@ nextflow_pipeline {
             def versions = removeNextflowVersion("$outputDir/pipeline_info/nallo_software_mqc_versions.yml")
             assertAll(
                 { assert workflow.success },
-                { assert !versions.containsKey('HIFIASM') },
+                { assert !versions.containsKey('HIFIASM_ASSEMBLY') },
                 { assert !versions.containsKey('SPLITUBAM') },
                 { assert stable_name.contains('aligned_reads') },
                 { assert snapshot(
@@ -224,7 +224,7 @@ nextflow_pipeline {
             def versions = removeNextflowVersion("$outputDir/pipeline_info/nallo_software_mqc_versions.yml")
             assertAll(
                 { assert workflow.success },
-                { assert versions.containsKey('HIFIASM') },
+                { assert versions.containsKey('HIFIASM_ASSEMBLY') },
                 { assert !versions.containsKey('SPLITUBAM') },
                 { assert !stable_name.contains('aligned_reads') },
                 { assert snapshot(
diff --git a/tests/samplesheet_stub.nf.test.snap b/tests/samplesheet_stub.nf.test.snap
index 1b14827d0..c9f4c3b60 100644
--- a/tests/samplesheet_stub.nf.test.snap
+++ b/tests/samplesheet_stub.nf.test.snap
@@ -148,15 +148,15 @@
                 "snvs/sample/HG002_Revio/HG002_Revio_deepvariant_snvs.vcf.gz.tbi"
             ]
         ],
-        "timestamp": "2026-04-02T14:16:09.579462317",
+        "timestamp": "2026-04-10T11:02:01.308163626",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test skip sex check - unknown sex": {
         "content": [
-            34,
+            35,
             {
                 "BCFTOOLS_MERGE": {
                     "bcftools": 1.22
@@ -182,7 +182,10 @@
                 "GUNZIP_FASTA": {
                     "gunzip": 1.13
                 },
-                "HIFIASM": {
+                "HIFIASM_ASSEMBLY": {
+                    "hifiasm": "0.25.0-r726"
+                },
+                "HIFIASM_BINS": {
                     "hifiasm": "0.25.0-r726"
                 },
                 "MINIMAP2_ALIGN": {
@@ -302,15 +305,15 @@
                 "qc/sambamba_depth/HG002_Revio/HG002_Revio_sambamba_depth.bed"
             ]
         ],
-        "timestamp": "2026-04-02T15:08:20.04740971",
+        "timestamp": "2026-04-10T11:06:15.116929482",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test sawfish with force_sawfish_joint_call_single_samples true": {
         "content": [
-            58,
+            59,
             {
                 "BCFTOOLS_CONCAT": {
                     "bcftools": 1.21
@@ -366,7 +369,10 @@
                 "GUNZIP_FASTA": {
                     "gunzip": 1.13
                 },
-                "HIFIASM": {
+                "HIFIASM_ASSEMBLY": {
+                    "hifiasm": "0.25.0-r726"
+                },
+                "HIFIASM_BINS": {
                     "hifiasm": "0.25.0-r726"
                 },
                 "MINIMAP2_ALIGN": {
@@ -522,10 +528,10 @@
                 "visualization_tracks/test/test_maf_sawfish.bw"
             ]
         ],
-        "timestamp": "2026-03-27T17:20:18.799744261",
+        "timestamp": "2026-04-10T11:03:44.925424818",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test alignment without genome assembly, --alignment_processes 1 and only plot chromograph coverage": {
@@ -627,15 +633,15 @@
                 "qc/somalier/relate/test/test.samples.tsv"
             ]
         ],
-        "timestamp": "2026-03-27T17:19:12.900562897",
+        "timestamp": "2026-04-10T11:02:48.417136378",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test genome assembly without alignment": {
         "content": [
-            16,
+            17,
             {
                 "GFASTATS": {
                     "gfastats": "1.3.11"
@@ -643,7 +649,10 @@
                 "GUNZIP_FASTA": {
                     "gunzip": 1.13
                 },
-                "HIFIASM": {
+                "HIFIASM_ASSEMBLY": {
+                    "hifiasm": "0.25.0-r726"
+                },
+                "HIFIASM_BINS": {
                     "hifiasm": "0.25.0-r726"
                 },
                 "MINIMAP2_ALIGN": {
@@ -691,10 +700,10 @@
                 "pipeline_info/nallo_software_mqc_versions.yml"
             ]
         ],
-        "timestamp": "2026-03-27T17:19:40.14872124",
+        "timestamp": "2026-04-10T11:03:11.069812239",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test Sentieon SNV calling with mock resources": {
@@ -850,10 +859,10 @@
                 "snvs/sample/HG002_Revio/HG002_Revio_sentieon_snvs.vcf.gz.tbi"
             ]
         ],
-        "timestamp": "2026-03-27T17:21:50.911562897",
+        "timestamp": "2026-04-10T11:05:07.164904359",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test CADD with mock resources": {
@@ -1029,10 +1038,10 @@
                 "snvs/sample/HG002_Revio/HG002_Revio_deepvariant_snvs.vcf.gz.tbi"
             ]
         ],
-        "timestamp": "2026-04-09T09:31:48.809555323",
+        "timestamp": "2026-04-10T11:01:27.560128811",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test Chromograph works without SNV annotation": {
@@ -1274,10 +1283,10 @@
                 "visualization_tracks/HG002_Revio/HG002_Revio_hificnv.maf.bw"
             ]
         ],
-        "timestamp": "2026-04-02T14:06:48.773434341",
+        "timestamp": "2026-04-10T11:05:48.396100192",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test Peddy without annotation": {
@@ -1416,15 +1425,15 @@
                 "snvs/sample/HG002_Revio/HG002_Revio_deepvariant_snvs.vcf.gz.tbi"
             ]
         ],
-        "timestamp": "2026-04-09T09:43:56.411556429",
+        "timestamp": "2026-04-10T11:07:36.674984654",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test family id same as sample id": {
         "content": [
-            191,
+            192,
             {
                 "BCFTOOLS_CONCAT": {
                     "bcftools": 1.21
@@ -1557,7 +1566,10 @@
                 "GUNZIP_FASTA": {
                     "gunzip": 1.13
                 },
-                "HIFIASM": {
+                "HIFIASM_ASSEMBLY": {
+                    "hifiasm": "0.25.0-r726"
+                },
+                "HIFIASM_BINS": {
                     "hifiasm": "0.25.0-r726"
                 },
                 "HIFICNV": {
@@ -1930,10 +1942,10 @@
                 "visualization_tracks/HG002_Revio/HG002_Revio_pbcpgtools.hap2.bw"
             ]
         ],
-        "timestamp": "2026-03-27T17:21:15.838618761",
+        "timestamp": "2026-04-10T11:04:36.153042764",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test alignment without genome assembly": {
@@ -2003,10 +2015,10 @@
                 "qc/somalier/relate/test/test.samples.tsv"
             ]
         ],
-        "timestamp": "2026-03-27T17:18:42.518949999",
+        "timestamp": "2026-04-10T11:02:23.665187845",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     },
     "Test skip sex check - multisample": {
@@ -2321,10 +2333,10 @@
                 "visualization_tracks/HG004/HG004_pbcpgtools.hap2.bw"
             ]
         ],
-        "timestamp": "2026-04-02T14:09:21.641135839",
+        "timestamp": "2026-04-10T11:07:06.95171678",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
         }
     }
 }
\ No newline at end of file