Preparation for release 1.0.0

CHANGELOG.md

@@ -3,14 +3,64 @@
 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).
 
-## v1.0dev - [date]
+## [1.0.0](https://github.com/nf-core/reportho/releases/tag/1.0.0) - Marvelous Mainsail [2024-05-07]
 
-Initial release of nf-core/reportho, created with the [nf-core](https://nf-co.re/) template.
+Although its location and design may vary greatly, the mainsail is always a key source of propulsion for a ship.
+
+This is the initial release of nf-core/reportho, created with the [nf-core](https://nf-co.re/) template.
+
+### `Credits`
+
+The following people have made significant contributions to the release through design, development and review:
+
+- [Igor Trujnara](https://github.com/itrujnara)
+- [Luisa Santus](https://github.com/luisas)
+- [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa)
+- [Alessio Vignoli](https://github.com/alessiovignoli)
+
+We also thank everyone else from the nf-core community who has participated in planning and development.
 
 ### `Added`
 
+The pipeline was created. In particular, it has the following features:
+
+- fetching of ortholog predictions from public databases, through APIs and from local snapshots
+- systematic comparison of the predictions and calculation of comparison statistics
+- creation of an ortholog list with user-defined criteria
+- basic downstream analysis of the obtained ortholog list
+- generation of a human-readable report
+
 ### `Fixed`
 
+Nothing yet.
+
 ### `Dependencies`
 
+The pipeline has the following notable dependencies:
+
+| Program         | Version |
+| --------------- | ------- |
+| Python          | 3.11.0  |
+| Python Requests | 2.31.0  |
+| Biopython       | 1.83    |
+| R               | 4.3.3   |
+| PyYAML          | 5.4.1   |
+| T-COFFEE        | 13.46.0 |
+| pigz            | 2.8     |
+| csvtk           | 0.26.0  |
+| Node            | 21.6.2  |
+| Yarn            | 1.22.19 |
+| React           | 18.3.1  |
+
+At release date, the following database versions were current:
+
+| Database       | Version       |
+| -------------- | ------------- |
+| OMA            | Jul2023       |
+| PANTHER        | 18            |
+| OrthoInspector | Eukaryota2023 |
+| EggNOG         | 5.0           |
+
 ### `Deprecated`
+
+Nothing.

README.md

@@ -18,9 +18,6 @@
 
 ## Introduction
 
-> [!WARNING]
-> This pipeline is still in active development. While the overall design will remain stable, all technical details, such as parameter names, are subject to change without notice.
-
 **nf-core/reportho** is a bioinformatics pipeline that compares and assembles orthology predictions for a query protein. It fetches ortholog lists for a query (or its closest annotated homolog) from public sources, calculates pairwise and global agreement, and generates a consensus list with the desired level of confidence. Optionally, it offers common analysis on the consensus orthologs, such as MSA and phylogeny reconstruction. Additionally, it generates a clean, human-readable report of the results.
 
 <!-- Tube map -->

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/reportho/tree/dev" target="_blank">nf-core/reportho</a>
+  This report has been generated by the <a href="https://github.com/nf-core/reportho/releases/tag/1.0.0" 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/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/reportho/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-reportho-methods-description":
     order: -1000

modules.json

@@ -51,7 +51,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -61,7 +61,7 @@
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     }
                 }

modules/local/make_report.nf

@@ -54,7 +54,7 @@ process MAKE_REPORT {
     ${task.process}:
         Node: \$(node --version)
         Yarn: \$(yarn --version)
-        React: \$(yarn view react version)
+        React: \$(yarn info react version | cut -d $'\n' -f 2)
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """

nextflow.config

@@ -244,7 +244,7 @@ manifest {
     description     = """A pipeline for ortholog fetching and analysis"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0dev'
+    version         = '1.0.0'
     doi             = ''
 }