Merge branch 'dev' into merging-template-updates

genomic-medicine-sweden · Jan 17, 2025 · da38fd8 · da38fd8
2 parents cd2c25b + 3198ff6
commit da38fd8
Show file tree

Hide file tree

Showing 13 changed files with 208 additions and 47 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#516](https://github.com/genomic-medicine-sweden/nallo/pull/516) - Added beta support for ONT R10 assembly
 - [#531](https://github.com/genomic-medicine-sweden/nallo/pull/531) - Added missing credits to the README
 
 ### `Changed`
@@ -19,8 +20,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter | New parameter |
-| ------------- | ------------- |
+| Old parameter | New parameter      |
+| ------------- | ------------------ |
+|               | `--hifiasm_preset` |
 
 > [!NOTE]
 > Parameter has been updated if both old and new parameter information is present.
@@ -29,8 +31,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Module updates
 
-| Tool | Old version | New version |
-| ---- | ----------- | ----------- |
+| Tool    | Old version | New version |
+| ------- | ----------- | ----------- |
+| hifiasm | 0.19.8      | 0.24.0      |
 
 > [!NOTE]
 > Version has been updated if both old and new version information is present.

diff --git a/README.md b/README.md
@@ -24,7 +24,7 @@
 ##### Alignment & assembly
 
 - Align reads to reference with [minimap2](https://github.com/lh3/minimap2)
-- Assemble haploid genomes with [hifiasm](https://github.com/chhylp123/hifiasm) (HiFi only)
+- Assemble 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
 

diff --git a/conf/modules/genome_assembly.config b/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(' ') }

diff --git a/modules.json b/modules.json
@@ -146,8 +146,9 @@
                     },
                     "hifiasm": {
                         "branch": "master",
-                        "git_sha": "daa15d5226111e10ca95c0d4a85fa6bd11a08a01",
-                        "installed_by": ["modules"]
+                        "git_sha": "6bb8be8a75d05ee6d31205b2b97d48c7bcef60ab",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/hifiasm/hifiasm.diff"
                     },
                     "longphase/haplotag": {
                         "branch": "master",

diff --git a/modules/nf-core/hifiasm/environment.yml b/modules/nf-core/hifiasm/environment.yml
diff --git a/modules/nf-core/hifiasm/hifiasm.diff b/modules/nf-core/hifiasm/hifiasm.diff
diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf
diff --git a/modules/nf-core/hifiasm/tests/main.nf.test.snap b/modules/nf-core/hifiasm/tests/main.nf.test.snap
diff --git a/nextflow.config b/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        = ''

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -451,6 +451,12 @@
                     "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,

diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
@@ -121,7 +121,7 @@
                     "gunzip": 1.1
                 },
                 "HIFIASM": {
-                    "hifiasm": "0.20.0-r639"
+                    "hifiasm": "0.24.0-r702"
                 },
                 "HIFICNV": {
                     "hificnv": "1.0.0-36e6461"

diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -121,7 +121,7 @@
                     "gunzip": 1.1
                 },
                 "HIFIASM": {
-                    "hifiasm": "0.20.0-r639"
+                    "hifiasm": "0.24.0-r702"
                 },
                 "HIFICNV": {
                     "hificnv": "1.0.0-36e6461"