Release v2.3.0

.nf-core.yml

@@ -11,4 +11,4 @@ template:
   name: pairgenomealign
   org: nf-core
   outdir: .
-  version: 2.2.3
+  version: 2.3.0

CHANGELOG.md

@@ -3,6 +3,41 @@
 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).
 
+## [v2.3.0](https://github.com/nf-core/pairgenomealign/releases/tag/2.3.0) "Umi budou" - [June 10th 2026]
+
+### `Added`
+
+- New `--multi_cram` option to produce a multi-query CRAM file combining all the alignments ([#60](https://github.com/nf-core/pairgenomealign/issues/60)).
+- New `--multiqc_thumbs` option to produce alignment thumbnails in the MultiQC report ([#93](https://github.com/nf-core/pairgenomealign/issues/93)).
+- New `--strand` option to index only one strand of the genome, which reduces memory usage at the expense of speed, and suppresses `-/+` alignments ([#97](https://github.com/nf-core/pairgenomealign/issues/97)).
+- New `--query` and `--queryName` convenience options to skip samplesheet creation when there is only one _query_ genome to align ([#112](https://github.com/nf-core/pairgenomealign/issues/112)).
+- In the GFF export format, the _target_ genome sequence lengths are now exported in `##sequence-region` fields ([#70](https://github.com/nf-core/pairgenomealign/issues/70)).
+
+### `Fixed`
+
+- Using the nf-core version of the `FASTA_BGZIP_INDEX_DICT_SAMTOOLS` subworkflow that we just contributed.
+- Check for input file existence in the parameter schema [#73](https://github.com/nf-core/pairgenomealign/issues/73)).
+
+### `Parameters`
+
+| Old parameter | New parameter      |
+| ------------- | ------------------ |
+|               | `--multi_cram`     |
+|               | `--multiqc_thumbs` |
+|               | `--query`          |
+|               | `--queryName`      |
+|               | `--strand`         |
+
+### `Dependencies`
+
+| Dependency          | Old version | New version |
+| ------------------- | ----------- | ----------- |
+| `SAMTOOLS_BGZIP`    | 1.21        |             |
+| `SAMTOOLS_DICT`     | 1.21        | 1.23.1      |
+| `SAMTOOLS_FAIDX`    | 1.21        | 1.23.1      |
+| `SAMTOOLS_MERGE`    |             | 1.23.1      |
+| `HTSLIB_BGZIPTABIX` |             | 1.23.1      |
+
 ## [v2.2.3](https://github.com/nf-core/pairgenomealign/releases/tag/2.2.3) "Reitou mikan" - [May 20th 2026]
 
 ### `Fixed`
@@ -28,6 +63,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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.
+- Display the _target_ genome length in the MultiQC report ([#77](https://github.com/nf-core/pairgenomealign/issues/77)).
 
 ### `Dependencies`
 

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/releases/tag/2.2.3" 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/2.2.3/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/2.3.0" 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/2.3.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pairgenomealign-methods-description":
     order: -1000

conf/modules.config

@@ -34,8 +34,8 @@ process {
         // -R01: uppercase all sequences and then lowercase simple repeats with tantan
         // -R10: keep original lowercase masking
         // -c: soft-mask lowercase letters
-        // -S2: index both strands
-        ext.args = { "${params.softmask=="tantan" ? '-R01' : '-R11'} -c -u${params.seed} -S2" }
+        // -S2: index both strands, -S1: index the forward strand only.
+        ext.args = { "${params.softmask=="tantan" ? '-R01' : '-R11'} -c -u${params.seed} ${params.strand=="both" ? '-S2' : '-S1'}" }
         publishDir = [
             enabled: false
         ]
@@ -111,6 +111,16 @@ process {
         ext.prefix = { "${meta.id}.m2m_plt_filtered" }
     }
 
+    withName: ALIGNMENT_CRAM {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: ALIGNMENT_MERGE {
+        ext.args = { "-O cram,version=3.0 --write-index" }
+    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
@@ -126,7 +136,23 @@ process {
         ]
     }
 
-    withName: 'SAMTOOLS_BGZIP' {
+    withName: 'MULTIQC_THUMBS' {
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + (175..177)) ? 'retry' : 'finish' } // override LAST_DOTPLOT to return to default.
+        ext.prefix    = { "${meta.id}.o2o_thumb" }
+        ext.args      = { "--sort2=3 --strands2=1 --width=${params.multiqc_thumbs} --height=${params.multiqc_thumbs} --fontsize=1 --border-pixel=0" }
+        publishDir    = [ enabled: false ]
+    }
+
+    withName: 'MULTIQC_THUMBS_HTML' {
+        publishDir = [
+            path: { "${params.outdir}/multiqc/alignment_thumbs" },
+            mode: params.publish_dir_mode,
+        ]
+    }
+
+    // FASTA_BGZIP_INDEX_DICT_SAMTOOLS subworkflow:
+
+    withName: 'HTSLIB_BGZIPTABIX' {
         publishDir = [
             path: { "${params.outdir}/alignment" },
             mode: params.publish_dir_mode,
@@ -144,7 +170,8 @@ process {
     withName: 'SAMTOOLS_DICT' {
         ext.args = { "-u ./${fasta} -a ${meta.id}" }
         publishDir = [
-            enabled: false
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
         ]
     }