nf-core · itrujnara · Oct 21, 2025 · Oct 16, 2025 · Oct 21, 2025 · Oct 21, 2025
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -17,4 +17,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 1.1.0
+  version: 1.2.0dev
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,8 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.2.0dev]() - TBD - [date]
+
 ## [v1.1.0](https://github.com/nf-core/reportho/releases/tag/1.1.0) - Reliable Rudder - [2025-10-21]
 
 The rudder is a control surface which is used to turn the ship. It is the main (and sometimes only) direct source of directional control.

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/reportho/releases/tag/1.1.0" target="_blank">nf-core/reportho</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/reportho/1.1.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/reportho/tree/dev" target="_blank">nf-core/reportho</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/reportho/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-reportho-methods-description":
     order: -1000

diff --git a/nextflow.config b/nextflow.config
@@ -300,7 +300,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.04.0'
-    version         = '1.1.0'
+    version         = '1.2.0dev'
     doi             = '10.5281/zenodo.11574565'
 }
 

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -21,8 +21,8 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2025-03-27T15:46:06+00:00",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2025-10-21T15:05:12+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-reportho_logo_hex_dark.png\">\n    <img alt=\"nf-core/reportho\" src=\"docs/images/nf-core-reportho_logo_hex_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/reportho/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/reportho/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/reportho/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/reportho/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/reportho/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.11574565-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.11574565)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/reportho)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23reportho-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/reportho)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/reportho** is a bioinformatics pipeline that compares and summarizes orthology predictions for one or a set of query proteins. For each query (or its closest annotated homolog), it fetches ortholog lists from public databases, identifies synonymous identifiers based on sequences, calculates the agreement of the obtained predictions (pairwise and global) and finally generates a consensus list of orthologs with the desired level of confidence. Additionally, it generates a clean, human-readable report of the results.\n\n<!-- Tube map -->\n\n![nf-core-reportho tube map](docs/images/reportho_tube_map.svg?raw=true \"nf-core-reportho tube map\")\n\n1. **Obtain Query Information**: identification of Uniprot ID and taxon ID for the query (or its closest homolog if the fasta file is used as input instead of the Uniprot ID).\n2. **Fetch Orthologs**: fetching of ortholog predictions from public databases, either through API or from local snapshot.\n\nSteps 3 and 4 can be skipped with `--skip_merge`.\n\n3. **Fetch Sequences**: fetching of sequences of identified orthologs.\n4. **Merge Synonymous Identifiers**: identification of synonymous identifiers based on sequence identity.\n5. **Compare and Assemble**: calculation of agreement statistics, creation of ortholog lists, selection of the consensus list.\n6. **Generate Report**: human-readable HTML report generation.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n:::warning\nDue to an nf-test issue outside our control, the current version of the pipeline is not tested with Conda. Most functionality should work with Conda, but we cannot guarantee it. We will rectify this issue as soon as possible.\n:::\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n```csv title=\"samplesheet_fasta.csv\"\nid,fasta\nBicD2,data/bicd2.fasta\nHBB,data/hbb.fasta\n```\n\nor if you know the UniProt ID of the protein you can provide it directly:\n\n```csv title=\"samplesheet.csv\"\nid,query\nBicD2,Q8TD16\nHBB,P68871\n```\n\n> [!NOTE]\n> If you provide both a FASTA file and a UniProt ID only the latter will be used.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/reportho \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/reportho/usage) and the [parameter documentation](https://nf-co.re/reportho/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/reportho/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/reportho/output).\n\n## Report image\n\nThe code to create the image producing the pipeline report is available under [this](https://github.com/itrujnara/orthologs-report) GitHub repository.\n\n## Credits\n\nnf-core/reportho was originally written by Igor Trujnara ([@itrujnara](https://github.com/itrujnara)).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Luisa Santus ([@luisas](https://github.com/luisas))\n- Alessio Vignoli ([@alessiovignoli](https://github.com/alessiovignoli))\n- Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa))\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#reportho` channel](https://nfcore.slack.com/channels/reportho) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/reportho for your analysis, please cite it using the following doi: [10.5281/zenodo.11574565](https://doi.org/10.5281/zenodo.11574565)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -105,7 +105,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#d47d3bf3-adf5-422a-8def-778c49257ec1"
+                    "@id": "#2fd35661-f8e7-4233-aaf7-777a5722790e"
                 }
             ],
             "name": "nf-core/reportho"
@@ -132,8 +132,13 @@
                 "SoftwareSourceCode",
                 "ComputationalWorkflow"
             ],
+            "creator": [
+                {
+                    "@id": "https://orcid.org/0000-0002-8735-5976"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2025-10-16T13:38:23Z",
+            "dateModified": "2025-10-21T17:05:12Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -146,6 +151,11 @@
             "license": [
                 "MIT"
             ],
+            "maintainer": [
+                {
+                    "@id": "https://orcid.org/0000-0002-8735-5976"
+                }
+            ],
             "name": [
                 "nf-core/reportho"
             ],
@@ -157,10 +167,10 @@
             },
             "url": [
                 "https://github.com/nf-core/reportho",
-                "https://nf-co.re/reportho/1.1.0/"
+                "https://nf-co.re/reportho/dev/"
             ],
             "version": [
-                "1.1.0"
+                "1.2.0dev"
             ]
         },
         {
@@ -176,11 +186,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#d47d3bf3-adf5-422a-8def-778c49257ec1",
+            "@id": "#2fd35661-f8e7-4233-aaf7-777a5722790e",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#e3694119-90a8-410f-afc2-c45ad009b0ac"
+                    "@id": "#15899387-82f8-43c2-9178-775a82d7aab4"
                 }
             ],
             "mainEntity": {
@@ -189,7 +199,7 @@
             "name": "Test suite for nf-core/reportho"
         },
         {
-            "@id": "#e3694119-90a8-410f-afc2-c45ad009b0ac",
+            "@id": "#15899387-82f8-43c2-9178-775a82d7aab4",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/reportho",
             "resource": "repos/nf-core/reportho/actions/workflows/nf-test.yml",
@@ -326,6 +336,12 @@
             "@type": "Organization",
             "name": "nf-core",
             "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "https://orcid.org/0000-0002-8735-5976",
+            "@type": "Person",
+            "email": "[email protected]",
+            "name": "Igor Trujnara"
         }
     ]
 }