Merge pull request #104 from nf-core/dev

Release 2.2.2

Author: takiifujita-ui

.nf-core.yml

@@ -11,4 +11,4 @@ template:
   name: pairgenomealign
   org: nf-core
   outdir: .
-  version: 2.2.2dev
+  version: 2.2.2

CHANGELOG.md

@@ -3,6 +3,26 @@
 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).
 
+## [v2.2.2](https://github.com/nf-core/pairgenomealign/releases/tag/2.2.2) "Juicy" - [January 30th 2026]
+
+### `Fixed`
+
+- Conforms to [nf-core template version `3.5.1`](https://nf-co.re/blog/2025/tools-3_5_0) ([#95](https://github.com/nf-core/pairgenomealign/issues/95), [#98](https://github.com/nf-core/pairgenomealign/issues/98)).
+- Fixed nf-core logo ([#90](https://github.com/nf-core/pairgenomealign/issues/90)).
+- Adjusted process requirements to `test_full` case ([#61](https://github.com/nf-core/pairgenomealign/issues/61)).
+- Set an icon in the `--targetName` option in the documentation ([#92](https://github.com/nf-core/pairgenomealign/issues/92)).
+- Fixed a bug of `last/train` records the wrong value for percent identity ([#96](https://github.com/nf-core/pairgenomealign/issues/96)).
+- Merged output channels in `last/dotplot` ([#100](https://github.com/nf-core/pairgenomealign/issues/100))
+- Created missing `meta.yml` for subworkflows ([#101](https://github.com/nf-core/pairgenomealign/issues/101)).
+- Exclude PNG files from pipeline test, because not reproducible in conda.
+
+### `Dependencies`
+
+| Dependency     | Old version | New version |
+| -------------- | ----------- | ----------- |
+| `assemblyscan` | 0.4.1       | 1.0.0       |
+| `MultiQC`      | 1.30        | 1.33        |
+
 ## [v2.2.1](https://github.com/nf-core/pairgenomealign/releases/tag/2.2.1) "C’est quoi ça?" - [August 5th 2025]
 
 ### `Fixed`

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/tree/dev" 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/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/2.2.2" 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/2.2.2/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pairgenomealign-methods-description":
     order: -1000

conf/modules.config

@@ -15,7 +15,6 @@ process {
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
     withName: 'ASSEMBLYSCAN' {
@@ -51,7 +50,6 @@ process {
         ext.prefix = { "${meta.id}.m2o_aln" }
         ext.args = { "-m${params.last_split_mismap}" }
     }
-
     withName: 'ALIGNMENT_SPLIT_O2O' {
         ext.prefix = { "${meta.id}.o2o_aln" }
         ext.args = { "--reverse -m${params.last_split_mismap}" }
@@ -118,15 +116,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'MULTIQC_ASSEMBLYSCAN_PLOT_DATA' {
         publishDir = [
             path: { "${params.outdir}/multiqc/assemblyscan_plot_data" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -140,7 +136,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/alignment" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename.equals('versions.yml') || filename.endsWith('.sizes')) ? null : filename }
+            saveAs: { filename -> (filename.endsWith('.sizes')) ? null : filename }
         ]
     }