Merge pull request #25 from nf-core/prepare_1_1_1

Prepare 1.1.1 release.

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.04.2"
+          - "24.10.1"
           - "latest-everything"
         profile:
           - "conda"

.nf-core.yml

@@ -13,4 +13,4 @@ template:
   name: pairgenomealign
   org: nf-core
   outdir: .
-  version: 1.1.0
+  version: 1.1.1

CHANGELOG.md

@@ -3,10 +3,15 @@
 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).
 
-## v1.1.0 "Nattou maki" - [September 27th, 2024]
+## [v1.1.1](https://github.com/nf-core/pairgenomealign/releases/tag/1.1.1) "Kani nabe" - [December 17th, 2024]
+
+This release brings the pipeline to the standards of Nextflow 24.10.1 and
+nf-core 3.1.0. No changes were made to the alignment process.
+
+## [v1.1.0](https://github.com/nf-core/pairgenomealign/releases/tag/1.1.0) "Nattou maki" - [September 27th, 2024]
 
 Added a new `softmask` parameter, to optionally keep original softmasking.
 
-## v1.0.0 "Sweet potato" - [August 27th, 2024]
+## [v1.0.0](https://github.com/nf-core/pairgenomealign/releases/tag/1.0.0) "Sweet potato" - [August 27th, 2024]
 
 Initial release of nf-core/pairgenomealign, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -6,10 +6,10 @@
 </h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/pairgenomealign/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/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/pairgenomealign/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/pairgenomealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/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/pairgenomealign/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13910535-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13910535)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.1-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

assets/multiqc_config.yml

@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/1.1.0" target="_blank">nf-core/pairgenomealign</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/pairgenomealign/1.1.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/1.1.1"
+  target="_blank">nf-core/pairgenomealign</a> analysis pipeline. For information about
+  how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/1.1.1/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pairgenomealign-methods-description":
     order: -1000
@@ -27,7 +28,11 @@ custom_data:
         title: "Substitution Percent Identity"
       "last -t":
         title: "Temperature"
-        description: "Parameter for converting between scores and probability ratios. This affects the column ambiguity estimates. A score is converted to a probability ratio by this formula: exp(score / TEMPERATURE). The default value is 1/lambda, where lambda is the scale factor of the scoring matrix, which is calculated by the method of Yu and Altschul (YK Yu et al. 2003, PNAS 100(26):15688-93)."
+        description: "Parameter for converting between scores and probability ratios.
+          This affects the column ambiguity estimates. A score is converted to a probability
+          ratio by this formula: exp(score / TEMPERATURE). The default value is 1/lambda,
+          where lambda is the scale factor of the scoring matrix, which is calculated
+          by the method of Yu and Altschul (YK Yu et al. 2003, PNAS 100(26):15688-93)."
       "last -a":
         title: "Gap existence"
         description: "Gap existence cost (lastal -a)"

nextflow.config

@@ -246,24 +246,28 @@ dag {
 
 manifest {
     name            = 'nf-core/pairgenomealign'
-    author          = """charles-plessy""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
-        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
-            name: 'charles-plessy',
-            affiliation: '',
-            email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            affiliation: 'Okinawa Institute of Science and Technology Graduate University (OIST)',
+            email: '[email protected]',
+            github: 'charles-plessy',
+            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: '0000-0001-7410-6295'
+        ],
+        [
+            affiliation: 'Okinawa Institute of Science and Technology Graduate University (OIST)',
+            email: '[email protected]',
+            github: 'U13bs1125',
+            contribution: ['contributor'],
             orcid: ''
         ],
     ]
     homePage        = 'https://github.com/nf-core/pairgenomealign'
     description     = """Pairwise alignment pipeline (genome to genome or reads to genome)"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=24.04.2'
-    version         = '1.1.0'
+    nextflowVersion = '!>=24.10.1'
+    version         = '1.1.1'
     doi             = ''
 }