Assemble ONT genomes

CHANGELOG.md

@@ -101,6 +101,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed one `single_sample` to `sample` and one `multi_sample` to `family` output directories missed in [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502)
 - [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed all `*_snv_*` to `*_snvs_*` for published output files to match `snvs`, `cnvs`, `svs` and `repeats`.
 - [#513](https://github.com/genomic-medicine-sweden/nallo/pull/513) - Updated CITATIONS.md link in README
+- [#](https://github.com/genomic-medicine-sweden/nallo/pull/) - Updated hifiasm to allow beta support for ONT R10 assembly
 
 ### `Removed`
 
@@ -162,6 +163,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | `--score_config_sv`              | `--genmod_score_config_svs`       |
 | `--parallel_alignments`          | `--alignment_processes`           |
 | `--svdb_dbs`                     | `--svdb_sv_databases`             |
+|                                  | `--hifiasm_preset`                |
 
 > [!NOTE]
 > Parameter has been updated if both old and new parameter information is present.
@@ -178,7 +180,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | genmod                | 3.8.2       | 3.9         |
 | WhatsHap              | 2.2         | 2.3         |
 | SVDB                  |             | 2.8.2       |
-| hifiasm               | 0.19.8      | 0.20.0      |
+| hifiasm               | 0.19.8      | 0.21.0      |
 | HiFiCNV               | 0.1.7       | 1.0.0       |
 | samtools/faidx        | 1.2         | 1.21        |
 | samtools/index        | 1.2         | 1.21        |

README.md

@@ -24,7 +24,7 @@
 ##### Alignment & assembly
 
 - Align reads to reference with [minimap2](https://github.com/lh3/minimap2)
-- Assemble (trio-binned) haploid genomes with [hifiasm](https://github.com/chhylp123/hifiasm) (HiFi only)
+- Assemble (trio-binned) haploid genomes with [hifiasm](https://github.com/chhylp123/hifiasm)
 
 ##### Variant calling
 
@@ -33,7 +33,7 @@
 - Call CNVs with [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV)
 - Call tandem repeats with [TRGT](https://github.com/PacificBiosciences/trgt/tree/main) (HiFi only)
 - Call paralogous genes with [Paraphase](https://github.com/PacificBiosciences/paraphase)
-- Call variants from assembly with [dipcall](https://github.com/lh3/dipcall) (HiFi only)
+- Call variants from assembly with [dipcall](https://github.com/lh3/dipcall)
 
 ##### Phasing and methylation
 

conf/modules/genome_assembly.config

@@ -27,6 +27,7 @@ process {
     withName: '.*:ASSEMBLY:HIFIASM' {
         ext.args = { [
             "${params.extra_hifiasm_options}",
+            "${params.hifiasm_preset}",
             "--dual-scaf",
             "--telo-m CCCTAA"
         ].join(' ') }

modules.json

@@ -146,8 +146,9 @@
                     },
                     "hifiasm": {
                         "branch": "master",
-                        "git_sha": "daa15d5226111e10ca95c0d4a85fa6bd11a08a01",
-                        "installed_by": ["modules"]
+                        "git_sha": "9c12c14558bb3b4ac7ee9542c268342782bacf9d",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/hifiasm/hifiasm.diff"
                     },
                     "longphase/haplotag": {
                         "branch": "master",

nextflow.config

@@ -34,7 +34,7 @@ params {
     somalier_sites               = null
 
     // Skip parts of the workflow
-    skip_genome_assembly         = params.preset == 'ONT_R10' ? true : false
+    skip_genome_assembly         = false
     skip_call_paralogs           = false
     skip_cnv_calling             = false
     skip_alignment               = false
@@ -49,6 +49,7 @@ params {
     skip_sv_annotation           = false
 
     deepvariant_model_type       = params.preset == 'ONT_R10' ? 'ONT_R104' : 'PACBIO'
+    hifiasm_preset               = params.preset == 'ONT_R10' ? '--ont' : ''
     minimap2_read_mapping_preset = params.preset == 'ONT_R10' ? 'lr:hq' : 'map-hifi'
     filter_snvs_expression       = ''
     filter_svs_expression        = ''

nextflow_schema.json

@@ -445,6 +445,12 @@
                     "enum": ["hifi-only", "trio-binning"],
                     "default": "hifi-only"
                 },
+                "hifiasm_preset": {
+                    "type": "string",
+                    "description": "Hifiasm preset, is set to `--ont` when `--profile ONT_R10` is active.",
+                    "enum": ["", "--ont"],
+                    "default": ""
+                },
                 "alignment_processes": {
                     "type": "integer",
                     "minimum": 1,

tests/samplesheet.nf.test.snap

@@ -121,7 +121,7 @@
                     "gunzip": 1.1
                 },
                 "HIFIASM": {
-                    "hifiasm": "0.20.0-r639"
+                    "hifiasm": "0.21.0-r686"
                 },
                 "HIFICNV": {
                     "hificnv": "1.0.0-36e6461"
@@ -670,6 +670,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-22T15:33:19.851771321"
+        "timestamp": "2024-11-28T12:18:43.950517922"
     }
-}
+}

tests/samplesheet_multisample_bam.nf.test.snap

@@ -121,7 +121,7 @@
                     "gunzip": 1.1
                 },
                 "HIFIASM": {
-                    "hifiasm": "0.20.0-r639"
+                    "hifiasm": "0.21.0-r686"
                 },
                 "HIFICNV": {
                     "hificnv": "1.0.0-36e6461"
@@ -869,6 +869,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-22T15:15:01.966301935"
+        "timestamp": "2024-11-28T12:20:41.635458971"
     }
-}
+}