nf-core · ramprasadn · Jan 29, 2025 · Jan 28, 2025 · Jan 28, 2025 · Jan 28, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Update haplogrep to v3.2.2 [#672](https://github.com/nf-core/raredisease/pull/672)
 - d4 files are not generated by default anymore [#648](https://github.com/nf-core/raredisease/pull/648)
 - Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638)
 - Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
@@ -46,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | bcftools   | 1.18        | 1.20        |
 | ensemblvep | 112         | 110         |
 | genmod     | 3.8.2       | 3.9         |
+| haplogrep  | 2.4.0       | 3.2.2       |
 | mosdepth   | 0.3.6       | 0.3.8       |
 | multiqc    | 1.21        | 1.26        |
 | picard     | 3.1.1       | 3.3.0       |

diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config
@@ -62,7 +62,8 @@ process {
         ext.prefix = { "${meta.prefix}" }
     }
 
-    withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP2_CLASSIFY_MT' {
+    withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT' {
+        ext.args   = '--tree [email protected]'
         ext.prefix = { "${meta.prefix}_haplogrep" }
         publishDir = [
             path: { "${params.outdir}/annotate_snv/mitochondria" },

diff --git a/modules.json b/modules.json
@@ -277,9 +277,9 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "haplogrep2/classify": {
+                    "haplogrep3/classify": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6af333190d76295671e4374df74513bdd7d1c596",
                         "installed_by": ["modules"]
                     },
                     "hmtnote/annotate": {

diff --git a/...-core/haplogrep2/classify/environment.yml → ...-core/haplogrep3/classify/environment.yml b/...-core/haplogrep2/classify/environment.yml → ...-core/haplogrep3/classify/environment.yml
diff --git a/modules/nf-core/haplogrep2/classify/main.nf → modules/nf-core/haplogrep3/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf → modules/nf-core/haplogrep3/classify/main.nf
diff --git a/modules/nf-core/haplogrep2/classify/meta.yml → modules/nf-core/haplogrep3/classify/meta.yml b/modules/nf-core/haplogrep2/classify/meta.yml → modules/nf-core/haplogrep3/classify/meta.yml
diff --git a/...re/haplogrep2/classify/tests/main.nf.test → ...re/haplogrep3/classify/tests/main.nf.test b/...re/haplogrep2/classify/tests/main.nf.test → ...re/haplogrep3/classify/tests/main.nf.test
diff --git a/...plogrep2/classify/tests/main.nf.test.snap → ...plogrep3/classify/tests/main.nf.test.snap b/...plogrep2/classify/tests/main.nf.test.snap → ...plogrep3/classify/tests/main.nf.test.snap
diff --git a/modules/nf-core/haplogrep3/classify/tests/nextflow.config b/modules/nf-core/haplogrep3/classify/tests/nextflow.config
diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf
@@ -6,7 +6,7 @@ include { REPLACE_SPACES_IN_VCFINFO                      } from '../../modules/l
 include { TABIX_TABIX as TABIX_TABIX_VEP_MT              } from '../../modules/nf-core/tabix/tabix/main'
 include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE_MT       } from '../../modules/nf-core/tabix/bgziptabix/main'
 include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT                } from '../../modules/nf-core/ensemblvep/vep/main'
-include { HAPLOGREP2_CLASSIFY as HAPLOGREP2_CLASSIFY_MT  } from '../../modules/nf-core/haplogrep2/classify/main'
+include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT  } from '../../modules/nf-core/haplogrep3/classify/main'
 include { VCFANNO as VCFANNO_MT                          } from '../../modules/nf-core/vcfanno/main'
 include { ANNOTATE_CADD                                  } from './annotate_cadd'
 include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT       } from '../../modules/nf-core/tabix/bgziptabix/main'
@@ -99,19 +99,19 @@ workflow ANNOTATE_MT_SNVS {
         TABIX_TABIX_VEP_MT(ENSEMBLVEP_MT.out.vcf)
 
         // Running haplogrep2
-        HAPLOGREP2_CLASSIFY_MT(ch_haplogrep_in, "vcf.gz")
+        HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in)
 
         ch_versions = ch_versions.mix(ENSEMBLVEP_MT.out.versions)
         ch_versions = ch_versions.mix(TABIX_TABIX_VEP_MT.out.versions)
         ch_versions = ch_versions.mix(VCFANNO_MT.out.versions)
         ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions)
-        ch_versions = ch_versions.mix(HAPLOGREP2_CLASSIFY_MT.out.versions)
+        ch_versions = ch_versions.mix(HAPLOGREP3_CLASSIFY_MT.out.versions)
         ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO_MT.out.versions)
         ch_versions = ch_versions.mix(ZIP_TABIX_HMTNOTE_MT.out.versions)
         ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions)
 
     emit:
-        haplog    = HAPLOGREP2_CLASSIFY_MT.out.txt // channel: [ val(meta), path(txt) ]
+        haplog    = HAPLOGREP3_CLASSIFY_MT.out.txt // channel: [ val(meta), path(txt) ]
         vcf_ann   = ENSEMBLVEP_MT.out.vcf          // channel: [ val(meta), path(vcf) ]
         tbi       = TABIX_TABIX_VEP_MT.out.tbi     // channel: [ val(meta), path(tbi) ]
         report    = ENSEMBLVEP_MT.out.report       // channel: [ path(html) ]