nf-core · angelphanth · Feb 9, 2026 · Feb 9, 2026 · Feb 9, 2026 · Mar 12, 2026
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 
 [![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)
 [![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
@@ -99,8 +99,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -90,6 +90,17 @@ process {
         ]
     }
 
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:WGET_MROOT' {
+        ext.prefix = "HMM"
+        ext.suffix = "tar.gz"
+        ext.args   = '--no-check-certificate' // explicitly naming output
+        publishDir = [
+            path: { "${params.outdir}/downloaded_dbs/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:HMMSEARCH_PFAM' {
         ext.args   = { "-E ${params.hmmsearch_evalue_cutoff}" }
         publishDir = [
@@ -110,6 +121,17 @@ process {
         ]
     }
 
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:HMMSEARCH_MROOT' {
+        ext.args   = { "-E ${params.hmmsearch_evalue_cutoff}" }
+        publishDir = [
+            path: { "${params.outdir}/domain_annotation/mroot/" },
+            mode: params.publish_dir_mode,
+            pattern: "*.domtbl.gz",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+
     withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:FUNCTIONAL_ANNOTATION:ARIA2' {
         publishDir = [
             path: { "${params.outdir}/downloaded_dbs/" },

diff --git a/conf/test.config b/conf/test.config
@@ -27,6 +27,7 @@ params {
     // Domain annotation
     pfam_latest_link   = params.pipelines_testdata_base_path + 'proteinannotator/testdata/pfam/Pfam-A_test.hmm.gz'
     funfam_latest_link = params.pipelines_testdata_base_path + 'proteinannotator/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz'
+    mroot_latest_link  =  'https://pavlopoulos-lab.org/metagroot/DownloadHmm'
     // Functional annotation
     interproscan_db_url       = params.pipelines_testdata_base_path + 'proteinannotator/testdata/interproscan/interproscan_test.tar.gz'
     interproscan_applications = 'Hamap,TIGRFAM,sfld'

diff --git a/main.nf b/main.nf
@@ -46,6 +46,9 @@ workflow NFCORE_PROTEINANNOTATOR {
         params.skip_funfam,
         params.funfam_db,
         params.funfam_latest_link,
+        params.skip_mroot,
+        params.mroot_db,
+        params.mroot_latest_link,
         params.skip_interproscan,
         params.interproscan_db_url,
         params.interproscan_db,

diff --git a/modules.json b/modules.json
@@ -59,6 +59,11 @@
                         "branch": "master",
                         "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
                         "installed_by": ["modules"]
+                    },
+                    "wget": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"]
                     }
                 }
             },

diff --git a/modules/nf-core/wget/environment.yml b/modules/nf-core/wget/environment.yml
diff --git a/modules/nf-core/wget/main.nf b/modules/nf-core/wget/main.nf
diff --git a/modules/nf-core/wget/meta.yml b/modules/nf-core/wget/meta.yml
diff --git a/modules/nf-core/wget/tests/main.nf.test b/modules/nf-core/wget/tests/main.nf.test
diff --git a/modules/nf-core/wget/tests/main.nf.test.snap b/modules/nf-core/wget/tests/main.nf.test.snap
diff --git a/modules/nf-core/wget/tests/nextflow.config b/modules/nf-core/wget/tests/nextflow.config
diff --git a/nextflow.config b/nextflow.config
@@ -25,6 +25,9 @@ params {
     skip_funfam             = false
     funfam_db               = null
     funfam_latest_link      = "https://download.cathdb.info/cath/releases/all-releases/v4_3_0/sequence-data/funfam-hmm3-v4_3_0.lib.gz"
+    skip_mroot              = false
+    mroot_db                = null
+    mroot_latest_link       = "https://pavlopoulos-lab.org/metagroot/DownloadHmm"
     hmmsearch_evalue_cutoff = 0.001
 
     // Functional annotation

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -276,6 +276,23 @@
                     "default": "https://download.cathdb.info/cath/releases/all-releases/v4_3_0/sequence-data/funfam-hmm3-v4_3_0.lib.gz",
                     "description": "CATH hosted link to the latest available (v4_3_0) FunFam HMM database file."
                 },
+                "skip_mroot": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-ban",
+                    "description": "Skip the domain annotation with the MetagRoot database.",
+                    "help": "Skips the domain annotation of input sequence against a MetagRoot database."
+                },
+                "mroot_db": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "Path to an already installed MetagRoot HMM database (.tar.gz).",
+                    "help_text": "If left null and skip_mroot is false, the pipeline will start downloading the latest MetagRoot HMM library."
+                },
+                "mroot_latest_link": {
+                    "type": "string",
+                    "default": "https://pavlopoulos-lab.org/metagroot/DownloadHmm",
+                    "description": "MetagRoot hosted link to the latest available MetagRoot HMM database file."
+                },
                 "hmmsearch_evalue_cutoff": {
                     "type": "number",
                     "default": 0.001,